├── Martini_lipid_Benchmark ├── README.md ├── martini_benchmark.pdf ├── figure1_db_data.csv ├── figure1_dhh_data.csv ├── figure1_2dc_data.csv ├── figure1_apl_data.csv ├── martini_benchmark_dhh.csv ├── martini_benchmark_db.csv ├── martini_benchmark_2dc.csv └── martini_benchmark_apl.csv ├── .DS_Store ├── autobuild-lipid-properties.xlsx ├── tools ├── analysis_pipeline │ ├── .DS_Store │ ├── martini_electrons-M2.dat │ ├── martini_electrons.dat │ ├── qwrap.py │ ├── diffusion.py │ └── area_lipid_g5.py ├── CG-Martini-lipids-naming.xlsx ├── resources │ ├── system-cg-default-M2.top │ ├── system-cg-default-M3.top │ ├── martini_v2.x_new-rf-em.mdp │ ├── martini_v2.x_new-rf-eq2.mdp │ ├── martini_v2.x_new-rf-eq3.mdp │ ├── martini_v2.x_new-rf-eq1.mdp │ ├── martini_v2.x_new-rf-eq4.mdp │ ├── martini_v3.0_prod.mdp │ └── martini_v2.x_new-rf-prod.mdp └── README.md ├── ITPs ├── README.md ├── martini_v3.0.0_diglycerides_v2.itp ├── martini_v3.0.0_DOTAP_v2.itp ├── martini_v3.0.0_phospholipids_3,3-BMP_v2.itp ├── martini_v3.0.0_phospholipids_2,2-BMP_v2.itp ├── martini_v3.0.0_sterols_v1.itp ├── martini_v3.0.0_fattyacids_v2.itp ├── martini_v3.0.0_phospholipids_CL_v2.itp ├── martini_v3.0.0_monoglycerides_v2.itp ├── martini_v3.0.0_hydrocarbons_v2.itp ├── martini_v3.0.0_ions_v1.itp ├── martini_v3.0.0_ffbonded_v2.itp ├── martini_v3.0.0_triglycerides_v2.itp └── martini_v3.0.0_solvents_v1.itp ├── README.md └── LICENSE.txt /Martini_lipid_Benchmark/README.md: -------------------------------------------------------------------------------- 1 | ### Martini lipid Benchmark (MIB) 2 | -------------------------------------------------------------------------------- /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/HEAD/.DS_Store -------------------------------------------------------------------------------- /autobuild-lipid-properties.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/HEAD/autobuild-lipid-properties.xlsx -------------------------------------------------------------------------------- /tools/analysis_pipeline/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/HEAD/tools/analysis_pipeline/.DS_Store -------------------------------------------------------------------------------- /tools/CG-Martini-lipids-naming.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/HEAD/tools/CG-Martini-lipids-naming.xlsx -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/martini_benchmark.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/HEAD/Martini_lipid_Benchmark/martini_benchmark.pdf -------------------------------------------------------------------------------- /tools/resources/system-cg-default-M2.top: -------------------------------------------------------------------------------- 1 | ; Include forcefield parameters 2 | ; The actual location of these files might be different on your computer! 3 | #include "xPATHx/martini2/martini_v2.2.itp" 4 | #include "xPATHx/martini2/martini_v2.0_ions.itp" 5 | #include "xPATHx/martini2/martini_v2.0_lipids_all_201506.itp" 6 | 7 | 8 | [ system ] 9 | ; name 10 | lipids-sim 11 | 12 | [ molecules ] 13 | ; name number 14 | -------------------------------------------------------------------------------- /ITPs/README.md: -------------------------------------------------------------------------------- 1 | ## Usage Warning !! 2 | Put "martini_v3.0.0_ffbonded_v2.itp" before any other lipid topologies in the .top file 3 | 4 | ## ⚠️ Note 5 | The .itp files from the open beta are identical to those in the final release associated with the publication. 6 | 7 | No changes have been made to the parameters — only the naming and organization may differ. 8 | You can safely continue using the open beta files if you already have them in place. -------------------------------------------------------------------------------- /tools/analysis_pipeline/martini_electrons-M2.dat: -------------------------------------------------------------------------------- 1 | 47 2 | NC3 = 50 3 | NH3 = 25 4 | GL0 = 41 5 | PO4 = 55 6 | GL1 = 29 7 | GL2 = 30 8 | OH1 = 22 9 | AM2 = 23 10 | T1A = 22 11 | C1A = 32 12 | C2A = 32 13 | C3A = 32 14 | C4A = 32 15 | C5A = 32 16 | C6A = 32 17 | C1B = 32 18 | C2B = 32 19 | C3B = 32 20 | C4B = 32 21 | C5B = 32 22 | C6B = 32 23 | D1A = 30 24 | D2A = 30 25 | D3A = 30 26 | D4A = 30 27 | D5A = 30 28 | D6A = 30 29 | D1B = 30 30 | D2B = 30 31 | D3B = 30 32 | D4B = 30 33 | D5B = 30 34 | D6B = 30 35 | W = 40 36 | WF = 40 37 | NA = 10 38 | CL = 18 39 | CNO = 48 40 | ROH = 32 41 | R1 = 21 42 | R2 = 22 43 | R3 = 22 44 | R4 = 22 45 | R5 = 16 46 | R6 = 16 47 | C1 = 32 48 | C2 = 33 49 | -------------------------------------------------------------------------------- /tools/analysis_pipeline/martini_electrons.dat: -------------------------------------------------------------------------------- 1 | 48 2 | NC3 = 50 3 | NH3 = 25 4 | GL0 = 41 5 | PO4 = 55 6 | GL1 = 29 7 | GL2 = 30 8 | OH1 = 22 9 | AM1 = 22 10 | AM2 = 23 11 | T1A = 22 12 | C1A = 32 13 | C2A = 32 14 | C3A = 32 15 | C4A = 32 16 | C5A = 32 17 | C6A = 32 18 | C1B = 32 19 | C2B = 32 20 | C3B = 32 21 | C4B = 32 22 | C5B = 32 23 | C6B = 32 24 | D1A = 30 25 | D2A = 30 26 | D3A = 30 27 | D4A = 30 28 | D5A = 30 29 | D6A = 30 30 | D1B = 30 31 | D2B = 30 32 | D3B = 30 33 | D4B = 30 34 | D5B = 30 35 | D6B = 30 36 | W = 40 37 | WF = 40 38 | NA = 10 39 | CL = 18 40 | CNO = 48 41 | ROH = 32 42 | R1 = 21 43 | R2 = 22 44 | R3 = 22 45 | R4 = 22 46 | R5 = 16 47 | R6 = 16 48 | C1 = 32 49 | C2 = 33 50 | -------------------------------------------------------------------------------- /tools/resources/system-cg-default-M3.top: -------------------------------------------------------------------------------- 1 | ; Include forcefield parameters 2 | ; The actual location of these files might be different on your computer! 3 | #include "xPATHx/martini_v3.0.0.itp" 4 | #include "xPATHx/martini_v3.0.0_ffbonded_v2.itp" 5 | #include "xPATHx/martini_v3.0.0_ceramides_v2.itp" 6 | #include "xPATHx/martini_v3.0.0_phospholipids_PA_v2.itp" 7 | #include "xPATHx/martini_v3.0.0_phospholipids_PC_v2.itp" 8 | #include "xPATHx/martini_v3.0.0_phospholipids_PE_v2.itp" 9 | #include "xPATHx/martini_v3.0.0_phospholipids_PG_v2.itp" 10 | #include "xPATHx/martini_v3.0.0_phospholipids_PS_v2.itp" 11 | #include "xPATHx/martini_v3.0.0_phospholipids_PI_v2.itp" 12 | #include "xPATHx/martini_v3.0.0_phospholipids_SM_v2.itp" 13 | #include "xPATHx/martini_v3.0.0_plasmalogens_PA_v2.itp" 14 | #include "xPATHx/martini_v3.0.0_plasmalogens_PC_v2.itp" 15 | #include "xPATHx/martini_v3.0.0_plasmalogens_PE_v2.itp" 16 | #include "xPATHx/martini_v3.0.0_plasmalogens_PG_v2.itp" 17 | #include "xPATHx/martini_v3.0.0_plasmalogens_PS_v2.itp" 18 | #include "xPATHx/martini_v3.0.0_etherphospholipids_PA_v2.itp" 19 | #include "xPATHx/martini_v3.0.0_etherphospholipids_PC_v2.itp" 20 | #include "xPATHx/martini_v3.0.0_etherphospholipids_PE_v2.itp" 21 | #include "xPATHx/martini_v3.0.0_etherphospholipids_PG_v2.itp" 22 | #include "xPATHx/martini_v3.0.0_etherphospholipids_PS_v2.itp" 23 | #include "xPATHx/martini_v3.0_sterols_v1.0.itp" 24 | #include "xPATHx/martini_v3.0.0_solvents_v1.itp" 25 | #include "xPATHx/martini_v3.0.0_ions_v1.itp" 26 | 27 | [ system ] 28 | ; name 29 | lipids-sim 30 | 31 | [ molecules ] 32 | ; name number 33 | -------------------------------------------------------------------------------- /tools/analysis_pipeline/qwrap.py: -------------------------------------------------------------------------------- 1 | from MDAnalysis import transformations 2 | import MDAnalysis as mda 3 | import numpy as np 4 | import sys 5 | 6 | # Diffusion analysis - added to analysis_lipids by Balazs Fabian 7 | 8 | """ Create CoM trajectory and unwrap it correctly. 9 | The molecules must be whole. Otherwise, MDA has 10 | to make it so, which is slow. 11 | """ 12 | 13 | def qwrap(trp, xtc, out_gro, out_xtc, lipid_names_str): 14 | u = mda.Universe(trp, xtc) 15 | 16 | # Add transformation to make whole (slow!) 17 | if False: 18 | workflow = [transformations.unwrap(u.atoms)] 19 | u.trajectory.add_transformations(*workflow) 20 | 21 | # TODO: this must be general enough! 22 | membrane = u.select_atoms(f"resname {lipid_names_str}") 23 | 24 | # dummy CoM group for writing trajectory 25 | dummyCoMGroup = sum([ lipid.atoms[0] for lipid in membrane.residues ]) 26 | 27 | # write a gro file 28 | dummyCoMGroup.write(out_gro) 29 | 30 | # Perform the "0-th" step 31 | # xw: wrapped 32 | # xu: unwrapped 33 | xw_prev = np.array([ lipid.atoms.center_of_mass() for lipid in membrane.residues ]) 34 | xu_prev = xw_prev 35 | 36 | with mda.Writer(out_xtc, dummyCoMGroup.n_atoms) as W: 37 | for ts in u.trajectory: 38 | 39 | L = u.dimensions[:3] 40 | xw = np.array([ lipid.atoms.center_of_mass() for lipid in membrane.residues ]) 41 | 42 | delta = xw - xw_prev 43 | shift = np.floor(delta/L + 0.5)*L 44 | xu = xu_prev + delta - shift 45 | 46 | dummyCoMGroup.positions = xu 47 | W.write(dummyCoMGroup) 48 | 49 | # Update 50 | xw_prev = xw 51 | xu_prev = xu 52 | 53 | def main(): 54 | # Needs sims tpr, xtc, out com.gro name, out xtc name, and string list of lipid names 55 | qwrap(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5]) 56 | 57 | if __name__ == "__main__": 58 | main() 59 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # M3-Lipid-Parameters 2 | [![DOI](https://img.shields.io/badge/DOI-10.1021%2Facscentsci.5c00755-blue)](https://doi.org/10.1021/acscentsci.5c00755) 3 | 4 | Home of the Martini 3 lipid parameters. 5 | 6 | ## 📚 Cite Us 7 | If you use these parameters in your work, please cite: 8 | 9 | Pedersen, K. B.; Ingólfsson, H. I.; Ramirez-Echemendia, D. P.; Borges-Araújo, L.; Andreasen, M. D.; Empereur-Mot, C.; Melcr, J.; Ozturk, T. N.; Bennett, W. F. D.; Kjølbye, L. R.; Brasnett, C.; Corradi, V.; Khan, H. M.; Cino, E. A.; Crowley, J.; Kim, H.; Fábián, B.; Borges-Araújo, A. C.; Pavan, G. M.; Launay, G.; Lolicato, F.; Wassenaar, T. A.; Melo, M. N.; Thallmair, S.; Carpenter, T. S.; Monticelli, L.; Tieleman, D. P.; Schiøtt, B.; Souza, P. C. T.; Marrink, S. J. 10 | The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior. 11 | ACS Central Science (2025). https://doi.org/10.1021/acscentsci.5c00755 12 | 13 | ## ⚠️ Note 14 | The .itp files from the open beta are identical to those in the final release associated with the publication. 15 | 16 | No changes have been made to the parameters — only the naming and organization may differ. 17 | You can safely continue using the open beta files if you already have them in place. 18 | 19 | ## License 20 | 21 | The contents of this repository are distributed under the Apache 2.0 license. 22 | The full text of the license is available in the source repository. 23 | 24 | ## Feedback and Contributions 25 | 26 | The development of Martini lipids is done on [github]. If you encounter any problems please file an [issue]. 27 | Contributions are welcome as [pull requests]. Note however that the 28 | decision of whether or not contributions can give authorship on resulting 29 | academic work is left to our sole discretion. 30 | 31 | [github]: https://github.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters 32 | [issue]: https://github.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/issues 33 | [pull requests]: https://github.com/Martini-Force-Field-Initiative/M3-Lipid-Parameters/pulls 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_diglycerides_v2.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; - Diglycerides 3 | ; 4 | ; Please cite: 5 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 6 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 7 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 8 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 9 | ; 10 | ; Last updated: Jan-2025 by Kasper; 11 | ; Authors: Kasper B. Pedersen 12 | 13 | ;;;;;; Martini lipid topology for di-C18:1 DG (DODG), generated using: 14 | ; 15 | ; Molecular topology and mapping of indices: 16 | ; OH-GL1-C1A-D2A-C3A-C4A 17 | ; | 18 | ; GL2-C1B-D2B-C3B-C4B 19 | ; 20 | ; 1 - 2 - 4 - 5 - 6 - 7 21 | ; \ | 22 | ; 3 - 8 - 9- 10- 11 23 | ; 24 | 25 | [moleculetype] 26 | ; molname nrexcl 27 | DODG 1 28 | 29 | [atoms] 30 | ; id type resnr residu atom cgnr charge (mass) 31 | 1 TN6 1 DODG COH 1 0 32 | 2 SN4a 1 DODG GL1 2 0 33 | 3 SN4a 1 DODG GL2 3 0 34 | 4 C1 1 DODG C1A 4 0 35 | 5 C4h 1 DODG D2A 5 0 36 | 6 C1 1 DODG C3A 6 0 37 | 7 C1 1 DODG C4A 7 0 38 | 8 C1 1 DODG C1B 8 0 39 | 9 C4h 1 DODG D2B 9 0 40 | 10 C1 1 DODG C3B 10 0 41 | 11 C1 1 DODG C4B 11 0 42 | 43 | [bonds] 44 | ; i j name (using named bondtypes from martini_v3.0_ffbonded.itp) 45 | ; i j funct force.c. 46 | 1 2 b_COH_GL_def 47 | 1 3 b_COH_GL_def_long 48 | 2 3 b_GL_GL_glyc 49 | 2 4 b_GL_C1_glyc_5long 50 | 4 5 b_C1_C4_mid_5long 51 | 5 6 b_C4_C1_mid 52 | 6 7 b_C1_C1_end 53 | 3 8 b_GL_C1_glyc_5long 54 | 8 9 b_C1_C4_mid_5long 55 | 9 10 b_C4_C1_mid 56 | 10 11 b_C1_C1_end 57 | 58 | [angles] 59 | ; i j k name (using named angletypes from martini_v3.0_ffbonded.itp) 60 | ; i j k funct angle force.c. 61 | 1 2 4 a_COH_GL_C_def 62 | 3 2 4 a_GL_GL_C_glyc 63 | 2 3 8 a_GL_GL_C_glyc 64 | 2 4 5 a_GL_C1_C4_glyc 65 | 4 5 6 a_C1_C4_C1_def 66 | 5 6 7 a_C4_C1_C1_def 67 | 3 8 9 a_GL_C1_C4_glyc 68 | 8 9 10 a_C1_C4_C1_def 69 | 9 10 11 a_C4_C1_C1_def 70 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_DOTAP_v2.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; - DOTAP 3 | ; Collection of trimethylammonium propane Martini 3 lipids 4 | ; 5 | ; Please cite: 6 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 7 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 8 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 9 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 10 | ; 11 | ; Last updated: Jan-2025 by Kasper; 12 | ; Authors: Kasper B. Pedersen 13 | 14 | ;;;;;; Martini lipid topology for di-C18:1 trimethylammonium propane (DOTAP), generated using: 15 | ; 16 | ; Molecular topology and mapping of indices: 17 | ; +NC3-GL1-C1A-D2A-C3A-C4A 18 | ; | 19 | ; GL2-C1B-D2B-C3B-C4B 20 | ; 21 | ; 1 - 2 - 4 - 5 - 6 - 7 22 | ; \ | 23 | ; 3 - 8 - 9- 10- 11 24 | ; 25 | 26 | [moleculetype] 27 | ; molname nrexcl 28 | DOTAP 1 29 | 30 | [atoms] 31 | ; id type resnr residu atom cgnr charge (mass) 32 | 1 Q1 1 DOTAP NC3 1 1.0 33 | 2 SN4a 1 DOTAP GL1 2 0 34 | 3 SN4a 1 DOTAP GL2 3 0 35 | 4 C1 1 DOTAP C1A 4 0 36 | 5 C4h 1 DOTAP D2A 5 0 37 | 6 C1 1 DOTAP C3A 6 0 38 | 7 C1 1 DOTAP C4A 7 0 39 | 8 C1 1 DOTAP C1B 8 0 40 | 9 C4h 1 DOTAP D2B 9 0 41 | 10 C1 1 DOTAP C3B 10 0 42 | 11 C1 1 DOTAP C4B 11 0 43 | 44 | [bonds] 45 | ; i j name (using named bondtypes from martini_v3.0_ffbonded.itp) 46 | ; i j funct force.c. 47 | 1 2 b_NC3_GL_def 48 | 1 3 b_NC3_GL_def_long 49 | 2 3 b_GL_GL_glyc 50 | 2 4 b_GL_C1_glyc_5long 51 | 4 5 b_C1_C4_mid_5long 52 | 5 6 b_C4_C1_mid 53 | 6 7 b_C1_C1_end 54 | 3 8 b_GL_C1_glyc_5long 55 | 8 9 b_C1_C4_mid_5long 56 | 9 10 b_C4_C1_mid 57 | 10 11 b_C1_C1_end 58 | 59 | [angles] 60 | ; i j k name (using named angletypes from martini_v3.0_ffbonded.itp) 61 | ; i j k funct angle force.c. 62 | 1 2 4 a_NC3_GL_C_def 63 | 3 2 4 a_GL_GL_C_glyc 64 | 2 3 8 a_GL_GL_C_glyc 65 | 2 4 5 a_GL_C1_C4_glyc 66 | 4 5 6 a_C1_C4_C1_def 67 | 5 6 7 a_C4_C1_C1_def 68 | 3 8 9 a_GL_C1_C4_glyc 69 | 8 9 10 a_C1_C4_C1_def 70 | 9 10 11 a_C4_C1_C1_def 71 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_phospholipids_3,3-BMP_v2.itp: -------------------------------------------------------------------------------- 1 | ; Last update : Jan-2025 by Kasper 2 | ; please cite: 3 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 4 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 5 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 6 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 7 | 8 | ;;;;;; Martini lipid topology for 3,3' isomer C18:1/C18:1 BMP (DOB3) 9 | ; 10 | ; molecular topology and mapping of indices 11 | ; 12 | ; OH1-GL1-C1A-D2A-C3A-C4A 13 | ; / 14 | ; PO4 15 | ; \ 16 | ; OH2-GL2-C1B-D2B-C3B-C4B 17 | ; 18 | ; 2 - 3 - 4 - 5 - 6 - 7 19 | ; / 20 | ; 1 21 | ; \ 22 | ; 8 - 9 - 10 - 11 - 12 - 13 23 | ; 24 | 25 | [moleculetype] 26 | ; molname nrexcl 27 | DO3B 1 28 | 29 | [atoms] 30 | ; id type resnr residu atom cgnr charge 31 | 1 Q5 1 DO3B PO4 1 -1.0 32 | 2 TN6 1 DO3B OH1 2 0 33 | 3 SN4a 1 DO3B GL1 3 0 34 | 4 C1 1 DO3B C1A 4 0 35 | 5 C4h 1 DO3B D2A 5 0 36 | 6 C1 1 DO3B C3A 6 0 37 | 7 C1 1 DO3B C4A 7 0 38 | 8 TN6 1 DO3B OH2 8 0 39 | 9 SN4a 1 DO3B GL2 9 0 40 | 10 C1 1 DO3B C1B 10 0 41 | 11 C4h 1 DO3B D2B 11 0 42 | 12 C1 1 DO3B C3B 12 0 43 | 13 C1 1 DO3B C4B 13 0 44 | 45 | [bonds] 46 | ; i j 47 | 1 2 b_PO4_OH_33_bmp 48 | 2 3 b_OH_GL_33_bmp 49 | 3 4 b_GL_C1_glyc_5long 50 | 4 5 b_C1_C4_mid_5long 51 | 5 6 b_C4_C1_mid 52 | 6 7 b_C1_C1_end 53 | 1 8 b_PO4_OH_33_bmp 54 | 8 9 b_OH_GL_33_bmp 55 | 9 10 b_GL_C1_glyc_5long 56 | 10 11 b_C1_C4_mid_5long 57 | 11 12 b_C4_C1_mid 58 | 12 13 b_C1_C1_end 59 | 60 | [angles] 61 | ; using named angletypes from martini_v3.0_ffbonded.itp 62 | ; head group 63 | 1 2 3 a_PO4_OH_GL_33_bmp 64 | 1 8 9 a_PO4_OH_GL_33_bmp 65 | ;glycerol backbone 66 | 2 3 4 a_OH_GL_C_33_bmp 67 | 8 9 10 a_OH_GL_C_33_bmp 68 | ; tails attached to glycerol 69 | 3 4 5 a_GL_C1_C4_glyc 70 | 9 10 11 a_GL_C1_C4_glyc 71 | ; tails 72 | 4 5 6 a_C1_C4_C1_def 73 | 5 6 7 a_C4_C1_C1_def 74 | 10 11 12 a_C1_C4_C1_def 75 | 11 12 13 a_C4_C1_C1_def 76 | 77 | -------------------------------------------------------------------------------- /tools/analysis_pipeline/diffusion.py: -------------------------------------------------------------------------------- 1 | import Dfit 2 | import numpy as np 3 | import MDAnalysis as mda 4 | import sys 5 | 6 | # Diffusion analysis - added to analysis_lipids by Balazs Fabian 7 | 8 | def diffusion(conf, traj, out_file, glsIntervalLower, glsIntervalUpper, lipid, leaflet_group): 9 | # Load trajectory 10 | #conf = sys.argv[1] 11 | #traj = sys.argv[2] 12 | u = mda.Universe(conf,traj) 13 | 14 | # Remove Center of Mass of the first frame 15 | #pos = u.atoms.positions - u.atoms.center_of_mass() 16 | pos = u.atoms.positions - u.atoms.center_of_geometry() # needed as MDAnalysis does not capture a mass in all cases current COM input conf .gro all have the same mass so this shoudl be ok 17 | u.atoms.positions = pos 18 | 19 | # Determine time step 20 | dt = u.trajectory.dt 21 | 22 | # Choose leaflet. 23 | # NOTE: after Center of Mass removal, 24 | # one leaflet must be at z<0 and the other at z>0 25 | if str(leaflet_group) == "0": 26 | symbol = "<" 27 | elif str(leaflet_group) == "1": 28 | symbol = ">" 29 | else: 30 | print(f"ERROR leaflet_group={leaflet_group} not supported") 31 | 32 | # Create selection for analysis 33 | # leaflet: the complete upper/lower leaflet irrespective of lipid type 34 | leaflet = u.select_atoms(f'prop z {symbol} 0') 35 | # sel: a single lipid type in the above leaflet 36 | sel = u.select_atoms(f'resname {lipid} and prop z {symbol} 0') 37 | 38 | # Remove CoM and convert to nm 39 | #pos = [ 0.1 * (sel.positions[:,:2] - leaflet.atoms.center_of_mass()[:2]) for ts in u.trajectory ] 40 | pos = [ 0.1 * (sel.positions[:,:2] - leaflet.atoms.center_of_geometry()[:2]) for ts in u.trajectory ] # see same change above 41 | pos = np.array(pos) 42 | pos = np.swapaxes(pos,0,1) 43 | # Convert to per-particle list 44 | pos = [ mol for mol in pos ] 45 | 46 | # Analyse using Dfit 47 | #print(f" Dfit.Dfit.Dcov(m=20,fz={pos},dt={dt},tmin={glsIntervalLower},tmax={glsIntervalUpper},fout={out_file},nitmax=200)") 48 | res = Dfit.Dfit.Dcov(m=20,fz=pos,dt=dt,tmin=int(glsIntervalLower),tmax=int(glsIntervalUpper),fout=out_file,nitmax=200) 49 | res.run_Dfit() 50 | res.analysis(tc=10*dt) 51 | 52 | def main(): 53 | diffusion(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6], sys.argv[7]) 54 | 55 | if __name__ == "__main__": 56 | main() 57 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_phospholipids_2,2-BMP_v2.itp: -------------------------------------------------------------------------------- 1 | ; Last update : Jan-2025 by Kasper 2 | ; please cite: 3 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 4 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 5 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 6 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 7 | 8 | ;;;;;; Martini lipid topology for 2,2' isomer C18:1/C18:1 BMP (DOB2) 9 | ; 10 | ; molecular topology and mapping of indices 11 | ; 12 | ; OH1 13 | ; | 14 | ; GL1-C1A-D2A-C3A-C4A 15 | ; / 16 | ; PO4 17 | ; \ 18 | ; GL2-C1B-D2B-C3B-C4B 19 | ; | 20 | ; OH2 21 | ; 22 | ; 3 23 | ; | 24 | ; 2 - 4 - 5 - 6 - 7 25 | ; / 26 | ; 1 27 | ; \ 28 | ; 8 - 10 - 11 - 12 - 13 29 | ; | 30 | ; 9 31 | 32 | [moleculetype] 33 | ; molname nrexcl 34 | DO2B 1 35 | 36 | [atoms] 37 | ; id type resnr residu atom cgnr charge 38 | 1 Q5 1 DO2B PO4 1 -1.0 39 | 2 SN4a 1 DO2B GL1 2 0 40 | 3 TN6 1 DO2B OH1 3 0 41 | 4 C1 1 DO2B C1A 4 0 42 | 5 C4h 1 DO2B D2A 5 0 43 | 6 C1 1 DO2B C3A 6 0 44 | 7 C1 1 DO2B C4A 7 0 45 | 8 SN4a 1 DO2B GL2 8 0 46 | 9 TN6 1 DO2B OH2 9 0 47 | 10 C1 1 DO2B C1B 10 0 48 | 11 C4h 1 DO2B D2B 11 0 49 | 12 C1 1 DO2B C3B 12 0 50 | 13 C1 1 DO2B C4B 13 0 51 | 52 | [bonds] 53 | ; i j 54 | 1 2 b_PO4_GL_def 55 | 2 3 b_GL_OH_22_bmp 56 | 2 4 b_GL_C1_glyc_5long 57 | 4 5 b_C1_C4_mid_5long 58 | 5 6 b_C4_C1_mid 59 | 6 7 b_C1_C1_end 60 | 1 8 b_PO4_GL_def 61 | 8 9 b_GL_OH_22_bmp 62 | 8 10 b_GL_C1_glyc_5long 63 | 10 11 b_C1_C4_mid_5long 64 | 11 12 b_C4_C1_mid 65 | 12 13 b_C1_C1_end 66 | 67 | [angles] 68 | ; using named angletypes from martini_v3.0_ffbonded.itp 69 | ; head group 70 | 1 2 3 a_PO4_GL_OH_22_bmp 71 | 1 8 9 a_PO4_GL_OH_22_bmp 72 | ;glycerol backbone 73 | 3 2 4 a_OH_GL_C_22_bmp 74 | 9 8 10 a_OH_GL_C_22_bmp 75 | 1 2 4 a_PO4_GL_C_def 76 | 1 8 10 a_PO4_GL_C_def 77 | ; tails attached to glycerol 78 | 2 4 5 a_GL_C1_C4_glyc 79 | 8 10 11 a_GL_C1_C4_glyc 80 | ; tails 81 | 4 5 6 a_C1_C4_C1_def 82 | 5 6 7 a_C4_C1_C1_def 83 | 10 11 12 a_C1_C4_C1_def 84 | 11 12 13 a_C4_C1_C1_def 85 | 86 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/figure1_db_data.csv: -------------------------------------------------------------------------------- 1 | lipid,temp_K,exp_db_nm,exp_db_err_nm,sim_db_nm,sim_db_err_nm 2 | DUPC,293.15,3.3,0.07,3.3078,0.0288 3 | DUPC,303.15,3.26,0.07,3.2443,0.0337 4 | DUPC,323.15,3.1,0.06,3.1271,0.0293 5 | DUPC,333.15,3.07,0.06,3.0937,0.0307 6 | DMPC,303.15,3.67,0.07,3.6308,0.0221 7 | DMPC,323.15,3.52,0.07,3.4647,0.0425 8 | DMPC,333.15,3.42,0.07,3.3552,0.0367 9 | DPPC,323.15,3.9,0.08,4.173,0.0475 10 | DPPC,333.15,3.81,0.08,4.0108,0.0169 11 | DSPC,333.15,4.22,0.08,4.527,0.0457 12 | MSPC,323.15,4.03,0.08,3.9029,0.0294 13 | SMPC,323.15,4.03,0.08,3.8696,0.0254 14 | PMPC,323.15,3.84,0.08,3.7955,0.0236 15 | DRPC,303.15,3.37,0.07,3.1463,0.0257 16 | DYPC,303.15,3.62,0.07,3.7106,0.0255 17 | DOPC,293.15,3.94,0.08,3.9193,0.0225 18 | DOPC,303.15,3.89,0.08,3.8435,0.0245 19 | DGPC,303.15,4.25,0.09,4.4299,0.0263 20 | DEPC,303.15,4.64,0.09,4.8149,0.0272 21 | POPC,293.15,3.98,0.08,4.1063,0.0328 22 | POPC,303.15,3.91,0.08,3.9954,0.0475 23 | POPC,323.15,3.79,0.08,3.8223,0.0265 24 | POPC,333.15,3.77,0.08,3.7537,0.0374 25 | SOPC,293.15,4.08,0.08,4.2514,0.0392 26 | SOPC,303.15,4.0,0.08,4.1156,0.0232 27 | SOPC,323.15,3.9,0.08,3.921,0.0294 28 | SOPC,333.15,3.85,0.08,3.8558,0.0221 29 | PDPC,293.15,3.74,0.07,3.8018,0.0285 30 | PDPC,303.15,3.68,0.07,3.7503,0.028 31 | PDPC,313.15,3.61,0.07,3.7032,0.0238 32 | SDPC,303.15,3.88,0.08,3.8702,0.0352 33 | PSM,318.15,3.84,0.08,4.069,0.0519 34 | PSM,328.15,3.75,0.08,3.9194,0.0318 35 | SSM,328.15,3.93,0.08,4.06,0.0389 36 | SSM,338.15,3.81,0.08,3.9377,0.0201 37 | DUPE,308.15,3.49,0.07,3.4043,0.0218 38 | DUPE,318.15,3.38,0.07,3.3574,0.0266 39 | DUPE,328.15,3.29,0.07,3.3129,0.0245 40 | POPE,308.15,4.05,0.08,4.3145,0.0264 41 | POPE,313.15,3.99,0.08,4.2352,0.0329 42 | POPE,323.15,3.88,0.08,4.0958,0.0295 43 | SOPE,308.15,4.31,0.09,4.3793,0.0433 44 | SOPE,313.15,4.26,0.09,4.2854,0.0363 45 | SOPE,323.15,4.13,0.08,4.1471,0.038 46 | DUPG,293.15,3.14,0.06,3.0018,0.0153 47 | DUPG,303.15,3.07,0.06,2.9535,0.0234 48 | DUPG,323.15,2.95,0.06,2.8704,0.0298 49 | DUPG,333.15,2.89,0.06,2.8288,0.0295 50 | DMPG,303.15,3.38,0.07,3.566,0.051 51 | DMPG,323.15,3.26,0.07,3.3887,0.0236 52 | DMPG,333.15,3.2,0.06,3.336,0.0401 53 | DPPG,323.15,3.67,0.07,4.1672,0.0417 54 | DPPG,333.15,3.59,0.07,4.0212,0.0424 55 | DSPG,333.15,3.91,0.08,4.4422,0.0696 56 | POPG,293.15,3.85,0.08,4.11,0.0464 57 | POPG,303.15,3.76,0.08,3.9875,0.0414 58 | POPG,323.15,3.61,0.07,3.8224,0.0187 59 | POPG,333.15,3.57,0.07,3.7411,0.0344 60 | SOPG,293.15,4.02,0.08,4.1952,0.0446 61 | SOPG,303.15,3.96,0.08,4.0914,0.0237 62 | SOPG,323.15,3.81,0.08,3.8944,0.0234 63 | SOPG,333.15,3.76,0.08,3.8158,0.0268 64 | DOPG,293.15,3.71,0.07,3.8951,0.0258 65 | DOPG,303.15,3.66,0.07,3.8333,0.0309 66 | DOPG,323.15,3.6,0.07,3.6925,0.017 67 | DOPG,333.15,3.59,0.07,3.645,0.0231 68 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/figure1_dhh_data.csv: -------------------------------------------------------------------------------- 1 | lipid,temp_K,exp_dhh_nm,exp_dhh_err_nm,sim_dhh_nm,sim_dhh_err_nm 2 | DUPC,293.15,3.0,0.06,3.0599,0.0947 3 | DUPC,303.15,2.96,0.06,3.0506,0.0828 4 | DUPC,323.15,2.96,0.06,2.9508,0.131 5 | DUPC,333.15,2.96,0.06,2.9225,0.1074 6 | DMPC,303.15,3.45,0.07,3.5014,0.0442 7 | DMPC,323.15,3.22,0.07,3.4483,0.0832 8 | DMPC,333.15,3.22,0.07,3.2623,0.083 9 | DPPC,323.15,3.86,0.08,4.0361,0.1039 10 | DPPC,333.15,3.46,0.07,3.8408,0.0896 11 | DSPC,333.15,4.33,0.09,4.3423,0.0682 12 | MSPC,323.15,3.57,0.07,3.8354,0.0728 13 | SMPC,323.15,3.48,0.07,3.7815,0.098 14 | PMPC,323.15,3.39,0.07,3.6653,0.0917 15 | DRPC,303.15,2.96,0.06,3.117,0.0996 16 | DYPC,303.15,3.21,0.06,3.554,0.1087 17 | DOPC,293.15,3.7,0.07,3.9106,0.1019 18 | DOPC,303.15,3.68,0.07,3.7756,0.1037 19 | DGPC,303.15,3.89,0.08,4.2817,0.1201 20 | DEPC,303.15,4.55,0.09,4.7647,0.1188 21 | POPC,293.15,3.74,0.07,3.9899,0.0742 22 | POPC,303.15,3.65,0.07,3.9072,0.0815 23 | POPC,323.15,3.6,0.07,3.7941,0.1084 24 | POPC,333.15,3.59,0.07,3.7216,0.07 25 | SOPC,293.15,3.85,0.08,4.1639,0.0532 26 | SOPC,303.15,3.86,0.08,4.0829,0.0846 27 | SOPC,323.15,3.7,0.07,3.9324,0.0552 28 | SOPC,333.15,3.58,0.07,3.8629,0.1194 29 | PDPC,293.15,3.32,0.07,3.6127,0.0482 30 | PDPC,303.15,3.3,0.07,3.6352,0.0996 31 | PDPC,313.15,3.22,0.06,3.692,0.1705 32 | SDPC,303.15,3.52,0.07,3.8106,0.1101 33 | PSM,318.15,3.89,0.08,3.9958,0.0952 34 | PSM,328.15,3.78,0.08,3.8871,0.0722 35 | SSM,328.15,4.0,0.08,4.0656,0.0768 36 | SSM,338.15,3.94,0.08,4.004,0.1237 37 | DUPE,308.15,3.35,0.07,3.1151,0.1053 38 | DUPE,318.15,3.25,0.07,3.0474,0.0885 39 | DUPE,328.15,3.15,0.06,2.9039,0.1301 40 | POPE,308.15,3.83,0.08,4.1379,0.0754 41 | POPE,313.15,3.74,0.07,4.0681,0.0997 42 | POPE,323.15,3.87,0.08,3.9825,0.1021 43 | SOPE,308.15,4.16,0.08,4.2824,0.0665 44 | SOPE,313.15,4.01,0.08,4.1322,0.06 45 | SOPE,323.15,3.98,0.08,4.0798,0.0814 46 | DUPG,293.15,3.0,0.06,2.7603,0.1297 47 | DUPG,303.15,2.94,0.06,2.783,0.1478 48 | DUPG,323.15,2.88,0.06,2.7078,0.176 49 | DUPG,333.15,2.84,0.06,2.6723,0.1388 50 | DMPG,303.15,3.46,0.07,3.4143,0.0917 51 | DMPG,323.15,3.46,0.07,3.344,0.1274 52 | DMPG,333.15,3.38,0.07,3.359,0.0974 53 | DPPG,323.15,3.86,0.08,3.9315,0.0771 54 | DPPG,333.15,3.76,0.08,3.8514,0.1685 55 | DSPG,333.15,4.12,0.08,4.3432,0.1074 56 | POPG,293.15,3.7,0.07,3.9467,0.1146 57 | POPG,303.15,3.66,0.07,3.8873,0.1519 58 | POPG,323.15,3.56,0.07,3.7143,0.1081 59 | POPG,333.15,3.54,0.07,3.6632,0.1519 60 | SOPG,293.15,3.88,0.08,4.1713,0.075 61 | SOPG,303.15,3.82,0.08,4.1036,0.0965 62 | SOPG,323.15,3.72,0.07,3.901,0.1163 63 | SOPG,333.15,3.66,0.07,3.7876,0.0685 64 | DOPG,293.15,3.58,0.07,3.9031,0.09 65 | DOPG,303.15,3.58,0.07,3.8411,0.1198 66 | DOPG,323.15,3.54,0.07,3.7784,0.0949 67 | DOPG,333.15,3.56,0.07,3.7139,0.0745 68 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/figure1_2dc_data.csv: -------------------------------------------------------------------------------- 1 | lipid,temp_K,exp_2dc_nm,exp_2dc_err_nm,sim_2dc_nm,sim_2dc_err_nm 2 | DUPC,293.15,2.19,0.04,2.2375,0.0196 3 | DUPC,303.15,2.17,0.04,2.2047,0.0138 4 | DUPC,323.15,2.08,0.04,2.1241,0.0105 5 | DUPC,333.15,2.06,0.04,2.1037,0.0138 6 | DMPC,303.15,2.57,0.05,2.5011,0.0119 7 | DMPC,323.15,2.48,0.05,2.3966,0.0223 8 | DMPC,333.15,2.41,0.05,2.3305,0.0236 9 | DPPC,323.15,2.85,0.06,3.1393,0.0282 10 | DPPC,333.15,2.79,0.06,3.0162,0.0161 11 | DSPC,333.15,3.19,0.06,3.3556,0.0331 12 | MSPC,323.15,2.91,0.06,2.8254,0.0161 13 | SMPC,323.15,2.92,0.06,2.7945,0.0132 14 | PMPC,323.15,2.7,0.05,2.7218,0.0113 15 | DRPC,303.15,2.34,0.05,2.1599,0.0522 16 | DYPC,303.15,2.62,0.05,2.7908,0.0113 17 | DOPC,293.15,3.0,0.06,2.8739,0.0188 18 | DOPC,303.15,2.9,0.06,2.8235,0.0187 19 | DGPC,303.15,3.26,0.07,3.4945,0.0382 20 | DEPC,303.15,3.64,0.07,3.7557,0.0161 21 | POPC,293.15,2.92,0.06,3.0628,0.0615 22 | POPC,303.15,2.88,0.06,2.9815,0.0769 23 | POPC,323.15,2.81,0.06,2.8598,0.0759 24 | POPC,333.15,2.8,0.06,2.8472,0.0452 25 | SOPC,293.15,3.04,0.06,3.114,0.027 26 | SOPC,303.15,2.99,0.06,3.0178,0.0151 27 | SOPC,323.15,2.93,0.06,2.8898,0.0186 28 | SOPC,333.15,2.9,0.06,2.8386,0.015 29 | PDPC,293.15,2.82,0.06,2.9191,0.0434 30 | PDPC,303.15,2.78,0.06,2.8927,0.0283 31 | PDPC,313.15,2.73,0.05,2.8653,0.0124 32 | SDPC,303.15,2.97,0.06,2.9224,0.0462 33 | PSM,318.15,2.93,0.06,3.1276,0.0302 34 | PSM,328.15,2.87,0.06,3.0235,0.024 35 | SSM,328.15,3.05,0.06,3.1511,0.0348 36 | SSM,338.15,2.97,0.06,3.0659,0.0191 37 | DUPE,308.15,2.54,0.05,2.3522,0.0125 38 | DUPE,318.15,2.47,0.05,2.3296,0.0126 39 | DUPE,328.15,2.41,0.05,2.2961,0.0128 40 | POPE,308.15,3.21,0.06,3.2557,0.0602 41 | POPE,313.15,3.16,0.06,3.1909,0.0485 42 | POPE,323.15,3.08,0.06,3.1197,0.0383 43 | SOPE,308.15,3.45,0.07,3.2598,0.0355 44 | SOPE,313.15,3.41,0.07,3.1932,0.0263 45 | SOPE,323.15,3.32,0.07,3.1055,0.0182 46 | DUPG,293.15,2.17,0.04,2.1031,0.0574 47 | DUPG,303.15,2.13,0.04,2.0817,0.0414 48 | DUPG,323.15,2.06,0.04,2.0465,0.0229 49 | DUPG,333.15,2.03,0.04,2.0276,0.007 50 | DMPG,303.15,2.45,0.05,2.4972,0.0243 51 | DMPG,323.15,2.37,0.05,2.3728,0.0141 52 | DMPG,333.15,2.34,0.05,2.3374,0.0234 53 | DPPG,323.15,2.77,0.06,3.1528,0.0314 54 | DPPG,333.15,2.72,0.05,3.0404,0.0345 55 | DSPG,333.15,3.04,0.06,3.2884,0.044 56 | POPG,293.15,2.91,0.06,3.1101,0.0541 57 | POPG,303.15,2.85,0.06,3.0298,0.0284 58 | POPG,323.15,2.76,0.06,2.9121,0.0133 59 | POPG,333.15,2.74,0.05,2.855,0.0153 60 | SOPG,293.15,3.1,0.06,3.0965,0.0366 61 | SOPG,303.15,3.05,0.06,3.0124,0.0161 62 | SOPG,323.15,2.95,0.06,2.8719,0.0162 63 | SOPG,333.15,2.92,0.06,2.8302,0.0314 64 | DOPG,293.15,2.85,0.06,2.8732,0.0193 65 | DOPG,303.15,2.82,0.06,2.8276,0.0138 66 | DOPG,323.15,2.79,0.06,2.7357,0.008 67 | DOPG,333.15,2.78,0.06,2.7038,0.0104 68 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/figure1_apl_data.csv: -------------------------------------------------------------------------------- 1 | lipid,temp_K,exp_apl_nm^2,exp_apl_err_nm^2,sim_apl_nm^2,sim_apl_err_nm^2 2 | DUPC,293.15,0.596,0.012,0.5508,0.0057 3 | DUPC,303.15,0.608,0.012,0.5647,0.0034 4 | DUPC,323.15,0.648,0.013,0.5964,0.0038 5 | DUPC,333.15,0.659,0.013,0.6102,0.0043 6 | DMPC,303.15,0.599,0.012,0.5694,0.0026 7 | DMPC,323.15,0.633,0.013,0.6063,0.0058 8 | DMPC,333.15,0.657,0.013,0.6304,0.0059 9 | DPPC,323.15,0.631,0.013,0.5579,0.0054 10 | DPPC,333.15,0.65,0.013,0.5863,0.0036 11 | DSPC,333.15,0.638,0.013,0.5651,0.0058 12 | MSPC,323.15,0.622,0.012,0.595,0.0047 13 | SMPC,323.15,0.62,0.012,0.6014,0.0041 14 | PMPC,323.15,0.629,0.013,0.5812,0.0026 15 | DRPC,303.15,0.642,0.01,0.6526,0.0046 16 | DYPC,303.15,0.658,0.01,0.6146,0.0029 17 | DOPC,293.15,0.643,0.013,0.6356,0.0043 18 | DOPC,303.15,0.669,0.01,0.6526,0.0045 19 | DGPC,303.15,0.666,0.01,0.6191,0.0032 20 | DEPC,303.15,0.657,0.01,0.6161,0.0032 21 | POPC,293.15,0.627,0.013,0.5778,0.0058 22 | POPC,303.15,0.643,0.013,0.5999,0.0057 23 | POPC,323.15,0.673,0.013,0.6376,0.0041 24 | POPC,333.15,0.681,0.014,0.6541,0.0048 25 | SOPC,293.15,0.638,0.013,0.5874,0.0049 26 | SOPC,303.15,0.655,0.013,0.6115,0.0032 27 | SOPC,323.15,0.681,0.013,0.6509,0.0048 28 | SOPC,333.15,0.694,0.014,0.6692,0.0045 29 | PDPC,293.15,0.693,0.013,0.6723,0.0038 30 | PDPC,303.15,0.711,0.014,0.6857,0.0059 31 | PDPC,313.15,0.729,0.015,0.7002,0.0032 32 | SDPC,303.15,0.704,0.014,0.695,0.0056 33 | PSM,318.15,0.6,0.012,0.5522,0.0051 34 | PSM,328.15,0.619,0.012,0.5764,0.0049 35 | SSM,328.15,0.625,0.013,0.5846,0.0073 36 | SSM,338.15,0.649,0.013,0.6073,0.0038 37 | DUPE,308.15,0.517,0.01,0.5253,0.0028 38 | DUPE,318.15,0.539,0.011,0.5372,0.0031 39 | DUPE,328.15,0.559,0.011,0.5502,0.0046 40 | POPE,308.15,0.58,0.012,0.545,0.0033 41 | POPE,313.15,0.592,0.012,0.5583,0.0048 42 | POPE,323.15,0.613,0.012,0.5808,0.0036 43 | SOPE,308.15,0.568,0.011,0.5634,0.0073 44 | SOPE,313.15,0.578,0.012,0.578,0.0048 45 | SOPE,323.15,0.601,0.012,0.5997,0.0041 46 | DUPG,293.15,0.602,0.012,0.6101,0.0039 47 | DUPG,303.15,0.621,0.012,0.6271,0.0046 48 | DUPG,323.15,0.653,0.013,0.6557,0.0074 49 | DUPG,333.15,0.671,0.013,0.6693,0.0025 50 | DMPG,303.15,0.625,0.013,0.5732,0.0067 51 | DMPG,323.15,0.66,0.013,0.6142,0.0041 52 | DMPG,333.15,0.675,0.014,0.6304,0.0076 53 | DPPG,323.15,0.647,0.013,0.5545,0.0059 54 | DPPG,333.15,0.668,0.013,0.5798,0.0063 55 | DSPG,333.15,0.668,0.013,0.5749,0.0085 56 | POPG,293.15,0.625,0.013,0.5752,0.007 57 | POPG,303.15,0.643,0.013,0.5975,0.0054 58 | POPG,323.15,0.684,0.014,0.6339,0.0044 59 | POPG,333.15,0.696,0.014,0.6513,0.004 60 | SOPG,293.15,0.629,0.013,0.591,0.0079 61 | SOPG,303.15,0.643,0.013,0.6111,0.0038 62 | SOPG,323.15,0.676,0.014,0.6531,0.0044 63 | SOPG,333.15,0.69,0.014,0.6706,0.0042 64 | DOPG,293.15,0.679,0.014,0.6347,0.0048 65 | DOPG,303.15,0.691,0.014,0.65,0.0035 66 | DOPG,323.15,0.711,0.014,0.6841,0.0024 67 | DOPG,333.15,0.717,0.014,0.6993,0.0032 68 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_sterols_v1.itp: -------------------------------------------------------------------------------- 1 | ; MARTINI 3 Cholesterol Version 1.0 (April 2023) 2 | ; by Luís Borges-Araújo; Ana C. Borges-Araújo; Tugba Nur Ozturk; Daniel P. Ramirez-Echemendia, 3 | ; Balázs Fábián, Timothy S. Carpenter; Sebastian Thallmair, Jonathan Barnoud; Helgi I. Ingólfsson; 4 | ; Gerhard Hummer; D. Peter Tieleman; Siewert J. Marrink; Paulo C. T. Souza; Manuel N. Melo. 5 | ; 6 | ; Martini 3 topology of Cholesterol. 7 | ; New Martini 3 cholesterol model, addressing issues related to its shape, volume, 8 | ; hydrophobicity, and temperature divergence resulting from the bonded setup. 9 | ; The proposed model mitigates some limitations of its Martini 2predecessor 10 | ; while maintaining or improving overall behavior as much as possible. 11 | ; 12 | ; Warning(s)/Note(s): 13 | ; Add define=-DFLEXIBLE to select harmonic bonds for minimization purposes. 14 | ; 15 | ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 16 | ; 17 | ; When using these parameters please read and cite the parameterization article: 18 | ; Borges-Araújo, L. et al. Martini 3 Coarse-Grained Force Field for cholesterol. (2023) doi:10.26434/chemrxiv-2023-lh7bq 19 | ; 20 | ; Also be sure to check https://github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters 21 | ; for updates to these parameters. 22 | ; 23 | ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 24 | 25 | [ moleculetype ] 26 | ; molname nrexcl 27 | CHOL 1 28 | 29 | [ atoms ] 30 | ; i type resnr residue atom cgnr charge mass 31 | 1 P1 1 CHOL ROH 1 0.0 0.0 32 | 2 SC4 1 CHOL R1 2 0.0 159.8 33 | 3 SC3 1 CHOL R2 3 0.0 157.0 34 | 4 SC3 1 CHOL R3 4 0.0 0.0 35 | 5 SC3 1 CHOL R4 5 0.0 0.0 36 | 6 TC2 1 CHOL R5 6 0.0 0.0 37 | 7 TC2 1 CHOL R6 7 0.0 0.0 38 | 8 C2 1 CHOL C1 8 0.0 115.2 39 | 9 C2 1 CHOL C2 9 0.0 72.0 40 | 41 | [ bonds ] 42 | ; i j funct length force 43 | 8 9 1 0.440 15000 44 | #ifdef FLEXIBLE 45 | 8 3 1 0.75012 100000 46 | 8 2 1 0.78504 100000 47 | 3 2 1 0.34797 100000 48 | #else 49 | [ constraints ] 50 | 8 3 1 0.75012 51 | 8 2 1 0.78504 52 | 3 2 1 0.34797 53 | #endif 54 | 55 | [ angles ] 56 | ; i j k funct angle force 57 | ; Cholesterol acyl chain angle 58 | 5 4 9 1 99.0 250 ;R4-R3-C2 59 | 60 | [ dihedrals ] 61 | ; i j k l funct angle force 62 | ; Cholesterol acyl chain tortion 63 | 7 5 4 9 2 -70.0 50 ;R6-R4-R3-C2 64 | 65 | [ virtual_sites3 ] 66 | 1 8 3 2 4 1.08999 0.35891 0.22947 67 | 4 8 3 2 4 -0.41067 0.83597 -0.05311 68 | 5 8 3 2 4 0.69138 -0.10352 0.17476 69 | 6 8 3 2 4 0.77524 0.22413 0.92700 70 | 7 8 3 2 4 0.06219 0.32398 0.76967 71 | 72 | [ exclusions ] 73 | ; i j k ... 74 | 1 2 3 4 5 6 7 8 75 | 2 3 4 5 6 7 8 76 | 3 4 5 6 7 8 77 | 4 5 6 7 8 78 | 5 6 7 8 79 | 6 7 8 80 | 7 8 81 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-em.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | 10 | ; TIMESTEP IN MARTINI 11 | ; Most simulations are numerically stable with dt=40 fs, 12 | ; however better energy conservation is achieved using a 13 | ; 20-30 fs timestep. 14 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 15 | 16 | ; define = -DFIX_UNDU -DPOSRES -DFLEXIBLE ; when hight field is added put undulations back in 17 | integrator = steep 18 | nsteps = 1500 ; 1500 normal 10 for .itp testing 19 | 20 | nstxout = 0 21 | nstvout = 0 22 | nstfout = 0 23 | nstlog = 1000 24 | nstenergy = 100 25 | nstxout-compressed = 1000 26 | compressed-x-precision = 100 27 | compressed-x-grps = 28 | energygrps = 29 | 30 | ; NEIGHBOURLIST and MARTINI 31 | ; To achieve faster simulations in combination with the Verlet-neighborlist 32 | ; scheme, Martini can be simulated with a straight cutoff. In order to 33 | ; do so, the cutoff distance is reduced 1.1 nm. 34 | ; Neighborlist length should be optimized depending on your hardware setup: 35 | ; updating ever 20 steps should be fine for classic systems, while updating 36 | ; every 30-40 steps might be better for GPU based systems. 37 | ; The Verlet neighborlist scheme will automatically choose a proper neighborlist 38 | ; length, based on a energy drift tolerance. 39 | ; 40 | ; Coulomb interactions can alternatively be treated using a reaction-field, 41 | ; giving slightly better properties. 42 | ; Please realize that electrostVatic interactions in the Martini model are 43 | ; not considered to be very accurate to begin with, especially as the 44 | ; screening in the system is set to be uniform across the system with 45 | ; a screening constant of 15. When using PME, please make sure your 46 | ; system properties are still reasonable. 47 | ; 48 | ; With the polarizable water model, the relative electrostatic screening 49 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 50 | ; apolar solvent. The polarizable water itself will perform the explicit screening 51 | ; in aqueous environment. In this case, the use of PME is more realistic. 52 | 53 | 54 | cutoff-scheme = Verlet 55 | nstlist = 20 56 | nsttcouple = 20 57 | nstpcouple = 20 58 | rlist = 1.35 59 | verlet-buffer-tolerance = -1 60 | ns_type = grid 61 | pbc = xyz 62 | 63 | coulombtype = reaction-field 64 | rcoulomb = 1.1 65 | epsilon_r = 15 ; 2.5 (with polarizable water) 66 | epsilon_rf = 0 67 | vdw_type = cutoff 68 | vdw-modifier = Potential-shift-verlet 69 | rvdw = 1.1 70 | 71 | ; MARTINI and CONSTRAINTS 72 | ; for ring systems and stiff bonds constraints are defined 73 | ; which are best handled using Lincs. 74 | 75 | constraints = none 76 | constraint_algorithm = Lincs 77 | lincs-order = 8 78 | lincs-iter = 2 79 | lincs-warnangle = 90 80 | -------------------------------------------------------------------------------- /tools/README.md: -------------------------------------------------------------------------------- 1 | # Tools 2 | 3 | This directory contains reusable pieces of code usually used in simulation tests and data analysis. 4 | 5 | It is encouraged to refactor code in a way that common pieces are contributed into this directory and 6 | then utilized by other pieces of code, scripts or notebooks 7 | rather than maintaining several independent copies or even different codes doing the same thing. 8 | 9 | Same rules (documentation, meaningful file names...) as to simulation tests also apply here. 10 | 11 | 12 | # Auto-generation tools 13 | 14 | For the auto-generation tools here is how to use them - please note these are being developed and are very preliminary. 15 | 16 | 1) Create a single lipid itp with lipid-itp-generator-Martini3-01.py. The generic -al flag specifies the arguments. Examples: 17 | - ./lipid-itp-generator-Martini3-01.py -alhead 'C P' -allink 'G G' -altail "CDCC cCCC" -alname POPC -o v1-POPC-lipid.itp 18 | - ./lipid-itp-generator-Martini3-01.py -alhead 'E P' -allink 'G G' -altail "CDCC cCCC" -alname POCE -o v1-POPE-lipid.itp 19 | - ./lipid-itp-generator-Martini3-01.py -alhead 'G P' -allink 'G G' -altail "CDCC cCCC" -alname POPG -o v1-POPG-lipid.itp 20 | - ./lipid-itp-generator-Martini3-01.py -alhead 'PI' -allink 'G G' -altail "DFFDD CCCC" -alname SDPI -o v1-SDPI-lipid.itp 21 | 22 | So far runs with the x40 tail combinations x5 headgroups PC, PE, PS, PG and PA as well as x10 tails for SM and CER and a few PI and PIP tails. 23 | Additionally, ether and plasmalogen lipids have been added with the same headgroup and tail combination as the glycerol ester phospholipids. 24 | **WARNING**: only limited tested has been done for many of these lipids. 25 | 26 | 27 | 2) Create .itp's for all/large number of lipids using generate-from-table-v02.py. Example: 28 | - python3 generate-from-table-v02.py -table CG-Martini3-lipids-naming-01.csv -makeItps yes -ofolder lipid_itps_v2/ 29 | 30 | **NOTE 1:** To choose a subset of lipids, copy CG-Martini3-lipids-naming-01.xlsx, select the desired lines, and save the table as .csv. Only lines with x and y in column 2 will be converted. 31 | 32 | **NOTE 2:** For the PI and PIPs the full comments and inositol sugars parameters are NOT autogenerated and need to be manually copied over. 33 | 34 | 3) Setup simulations using generate-from-table-v02.py . Example using Martini 3: 35 | - python3 ../tools/generate-from-table-v02.py -table ../tools/CG-Martini3-lipids-naming-01_test5.csv -CBT no -baseLipid POPC -setupSims yes 36 | 37 | Example using Martini 2: 38 | - python3 ../tools/generate-from-table-v02-M2-side-copy.py -table ../tools/CG-Martini2-lipids-naming-comparsion-to-M3.csv -CBT no -baseLipid POPC -setupSims yes 39 | 40 | **NOTE 1:** fixed box size for all simulations, results in 100 lipids in each leaflet, but variable size of water box depending on lipid size. 41 | 42 | **NOTE 2:** currently supports pure, POPC, DLPE and SSM-CHOL base where the x3 later mix 20% of lipid X into the base mixture 43 | 44 | 4) Run simulations: In run mode, generate-from-table-v02.py takes in the runner id and the number of runners that are running all the sims in this directory, e.g., one called the script runs all the simulation in current directory. 45 | **NOTE:** internal thread pool used to specify how many at a given time (currently set to x16 with -nt 2 for the GROMACS run command - so needs a threaded install of GROMACS). 46 | - python3 ../tools/generate-from-table-v02.py -table ../tools/CG-Martini3-lipids-naming-01_test5.csv -sRunId 0 -sRunC 1 -runSims yes 47 | 48 | But if you want to split over many nodes easy to, run one generate-from-table-v02.py per node and adjust -sRunId x -sRunC \ 49 | 50 | 5) Analysis of simulations: Run for one simulations - analysis pipeline uses x2 thread and has hardcoded variables - check analysis_lipids.py 51 | **NOTE 1:** need to install MDAnalysis, DiffusionGLS (https://github.com/bio-phys/DiffusionGLS.git) + add new modification, and FATSLiM, also edit FATSLiM path 52 | **NOTE 2:** the sim name is the M3_noCBT_POPC_DLPA/ (need to include /) 53 | Example: 54 | - python3 ../tools/analysis_pipeline/analysis_lipids.py M3_noCBT_POPC_DLPA/ 55 | 56 | To run the full set you can use generate-from-table-v02.py 57 | - python3 ../tools/generate-from-table-v02.py -table ../tools/CG-Martini3-lipids-naming-01_test5.csv -analyseSims yes 58 | 59 | 6) Scripts for slurm submisison: In tools/submit_slurm there are example slurm sbatch submission script for setup, run (submit_array.sh) and analysis (for Martini 3 as well as Martini 2 with M2 suffix). 60 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_fattyacids_v2.itp: -------------------------------------------------------------------------------- 1 | 2 | ;;;;; MARTINI 3.0 - Fatty Acids 3 | ;;;;; 4 | 5 | ; please cite: 6 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 7 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 8 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 9 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 10 | ; last edit Dec-2024, Kasper 11 | 12 | ;;;;; 13 | ;;;;; Oleic acid 14 | ;;;;; OA 15 | ;;;;; 16 | 17 | ;;;;; BEAD-INDEX MAPPING 18 | ;;;;; topology description 19 | ; 20 | ; COO-C1A-D2A-C3A-C4A 1-2-3-4-5 21 | ; 22 | 23 | [moleculetype] 24 | OA 1 25 | 26 | [atoms] 27 | ; id type resnr residu atom cgnr charge 28 | 1 SQ5n 1 OA COO 1 -1.0 29 | 2 C1 1 OA C1A 2 0 ; 5-1 mapping 30 | 3 C4h 1 OA D2A 3 0 31 | 4 C1 1 OA C3A 4 0 32 | 5 C1 1 OA C4A 5 0 33 | 34 | [bonds] 35 | ; i j funct length force.c. 36 | 1 2 b_COO_C1_fa_5long 37 | 2 3 b_C1_C4_mid_5long 38 | 3 4 b_C1_C4_mid 39 | 4 5 b_C1_C1_end 40 | 41 | [angles] 42 | 1 2 3 a_COO_C1_C4_fa 43 | 2 3 4 a_C1_C4_C1_def 44 | 3 4 5 a_C1_C1_C1_def 45 | 46 | ;;;;; 47 | ;;;;; Linoleic acid 48 | ;;;;; LA 49 | ;;;;; 50 | 51 | ;;;;; BEAD-INDEX MAPPING 52 | ;;;;; topology description 53 | ; 54 | ; COO-C1A-D2A-D3A-C4A 1-2-3-4-5 55 | 56 | [moleculetype] 57 | LA 1 58 | 59 | [atoms] 60 | ; id type resnr residu atom cgnr charge 61 | 1 SQ5n 1 LA COO 1 -1.0 62 | 2 C1 1 LA C1A 2 0 63 | 3 C4h 1 LA D2A 3 0 64 | 4 C4h 1 LA D3A 4 0 65 | 5 C1 1 LA C4A 5 0 66 | 67 | [bonds] 68 | ; i j funct length force.c. 69 | 1 2 b_COO_C1_fa_5long 70 | 2 3 b_C1_C4_mid_5long 71 | 3 4 b_C4_C4_mid 72 | 4 5 b_C1_C4_end 73 | 74 | [angles] 75 | 1 2 3 a_COO_C1_C4_fa 76 | 2 3 4 a_C1_C4_C4_def 77 | 3 4 5 a_C1_C4_C4_def 78 | 79 | ;;;;; 80 | ;;;;; α-linolenic acid (omega-3) 81 | ;;;;; LNA 82 | ;;;;; 83 | 84 | ;;;;; BEAD-INDEX MAPPING 85 | ;;;;; topology description 86 | ;;;;; 87 | ; 88 | ; COO-C1A-D2A-D3A-D4A 1-2-3-4-5 89 | 90 | [moleculetype] 91 | LNA 1 92 | 93 | [atoms] 94 | ; id type resnr residu atom cgnr charge 95 | 1 SQ5n 1 LNA COO 1 -1.0 96 | 2 C1 1 LNA C1A 2 0 97 | 3 C4h 1 LNA D2A 3 0 98 | 4 C4h 1 LNA D3A 4 0 99 | 5 C4h 1 LNA D4A 5 0 100 | 101 | [bonds] 102 | ; i j funct length force.c. 103 | 1 2 b_COO_C1_fa_5long 104 | 2 3 b_C1_C4_mid_5long 105 | 3 4 b_C4_C4_mid 106 | 4 5 b_C4_C4_end 107 | 108 | [angles] 109 | 1 2 3 a_COO_C1_C1_fa 110 | 2 3 4 a_C1_C4_C4_def 111 | 3 4 5 a_C4_C4_C4_def 112 | 113 | ;;;;; 114 | ;;;;; Myristic acid 115 | ;;;;; MA 116 | ;;;;; 117 | 118 | ;;;;; BEAD-INDEX MAPPING 119 | ;;;;; topology description 120 | ; 121 | ; COO-C1A-C2A-C3A 1-2-3-4 122 | 123 | [moleculetype] 124 | MA 1 125 | 126 | [atoms] 127 | ; id type resnr residu atom cgnr charge 128 | 1 SQ5n 1 MA COO 1 -1.0 129 | 2 C1 1 MA C1A 2 0 130 | 3 C1 1 MA C2A 3 0 131 | 4 C1 1 MA C3A 4 0 132 | 133 | [bonds] 134 | ; i j funct length force.c. 135 | 1 2 b_COO_C1_fa_5long 136 | 2 3 b_C1_C1_mid_5long 137 | 3 4 b_C1_C1_end 138 | 139 | [angles] 140 | 1 2 3 a_COO_C1_C1_fa 141 | 2 3 4 a_C1_C1_C1_def 142 | 143 | ;;;;; 144 | ;;;;; Palmitic acid 145 | ;;;;; PA 146 | ;;;;; 147 | 148 | ;;;;; BEAD-INDEX MAPPING 149 | ;;;;; topology description 150 | ; 151 | ; COO-C1A-C2A-C3A-C4A 1-2-3-4-5 152 | 153 | [moleculetype] 154 | PA 1 155 | 156 | [atoms] 157 | ; id type resnr residu atom cgnr charge 158 | 1 SQ5n 1 PA COO 1 -1.0 159 | 2 SC1 1 PA C1A 2 0 160 | 3 C1 1 PA C2A 3 0 161 | 4 C1 1 PA C3A 4 0 162 | 5 C1 1 PA C4A 5 0 163 | 164 | [bonds] 165 | ; i j funct length force.c. 166 | 1 2 b_COO_SC1_fa 167 | 2 3 b_SC1_C1_mid 168 | 3 4 b_C1_C1_mid 169 | 4 5 b_C1_C1_end 170 | 171 | [angles] 172 | 1 2 3 a_COO_C1_C1_fa 173 | 2 3 4 a_C1_C1_C1_def 174 | 3 4 5 a_C1_C1_C1_def 175 | 176 | ;;;;; 177 | ;;;;; Stearic acid 178 | ;;;;; SA 179 | ;;;;; 180 | 181 | ;;;;; BEAD-INDEX MAPPING 182 | ;;;;; topology description 183 | ; 184 | ; COO-C1A-C2A-C3A-C4A 1-2-3-4-5 185 | 186 | [moleculetype] 187 | SA 1 188 | 189 | [atoms] 190 | ; id type resnr residu atom cgnr charge 191 | 1 SQ5n 1 SA COO 1 -1.0 192 | 2 C1 1 SA C1A 2 0 193 | 3 C1 1 SA C2A 3 0 194 | 4 C1 1 SA C3A 4 0 195 | 5 C1 1 SA C4A 5 0 196 | 197 | [bonds] 198 | ; i j funct length force.c. 199 | 1 2 b_COO_C1_fa_5long 200 | 2 3 b_C1_C1_mid_5long 201 | 3 4 b_C1_C1_mid 202 | 4 5 b_C1_C1_end 203 | 204 | [angles] 205 | 1 2 3 a_COO_C1_C1_fa 206 | 2 3 4 a_C1_C1_C1_def 207 | 3 4 5 a_C1_C1_C1_def 208 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-eq2.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | title = Martini 10 | 11 | ; TIMESTEP IN MARTINI 12 | ; Most simulations are numerically stable with dt=40 fs, 13 | ; however better energy conservation is achieved using a 14 | ; 20-30 fs timestep. 15 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 16 | 17 | ; define = -DFIX_UNDU -DPOSRES -DFLEXIBLE ; when hight field is added put undulations back in 18 | integrator = md 19 | dt = 0.005 20 | nsteps = 20000 21 | 22 | nstxout = 0 23 | nstvout = 0 24 | nstfout = 0 25 | nstlog = 25000 26 | nstenergy = 25000 27 | nstxout-compressed = 25000 28 | compressed-x-precision = 100 29 | compressed-x-grps = 30 | energygrps = System 31 | 32 | ; NEIGHBOURLIST and MARTINI 33 | ; To achieve faster simulations in combination with the Verlet-neighborlist 34 | ; scheme, Martini can be simulated with a straight cutoff. In order to 35 | ; do so, the cutoff distance is reduced 1.1 nm. 36 | ; Neighborlist length should be optimized depending on your hardware setup: 37 | ; updating ever 20 steps should be fine for classic systems, while updating 38 | ; every 30-40 steps might be better for GPU based systems. 39 | ; The Verlet neighborlist scheme will automatically choose a proper neighborlist 40 | ; length, based on a energy drift tolerance. 41 | ; 42 | ; Coulomb interactions can alternatively be treated using a reaction-field, 43 | ; giving slightly better properties. 44 | ; Please realize that electrostVatic interactions in the Martini model are 45 | ; not considered to be very accurate to begin with, especially as the 46 | ; screening in the system is set to be uniform across the system with 47 | ; a screening constant of 15. When using PME, please make sure your 48 | ; system properties are still reasonable. 49 | ; 50 | ; With the polarizable water model, the relative electrostatic screening 51 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 52 | ; apolar solvent. The polarizable water itself will perform the explicit screening 53 | ; in aqueous environment. In this case, the use of PME is more realistic. 54 | 55 | 56 | cutoff-scheme = Verlet 57 | nstlist = 20 58 | nsttcouple = 20 59 | nstpcouple = 20 60 | rlist = 1.35 61 | verlet-buffer-tolerance = -1 62 | ns_type = grid 63 | pbc = xyz 64 | 65 | coulombtype = reaction-field 66 | rcoulomb = 1.1 67 | epsilon_r = 15 ; 2.5 (with polarizable water) 68 | epsilon_rf = 0 69 | vdw_type = cutoff 70 | vdw-modifier = Potential-shift-verlet 71 | rvdw = 1.1 72 | 73 | ; MARTINI and TEMPERATURE/PRESSURE 74 | ; normal temperature and pressure coupling schemes can be used. 75 | ; It is recommended to couple individual groups in your system separately. 76 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 77 | ; thermostat using a coupling constant of the order of 1 ps. Even better 78 | ; temperature control can be achieved by reducing the temperature coupling 79 | ; constant to 0.1 ps, although with such tight coupling (approaching 80 | ; the time step) one can no longer speak of a weak-coupling scheme. 81 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 82 | ; The Berendsen thermostat is less suited since it does not give 83 | ; a well described thermodynamic ensemble. 84 | ; 85 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 86 | ; with a coupling constant in the range 4-8 ps and typical compressibility 87 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 88 | ; the Berendsen barostat probably gives better results, as the Parrinello- 89 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 90 | ; coupling should be done semiisotropic. 91 | 92 | tcoupl = berendsen 93 | tc-grps = Solvent Rest 94 | tau_t = 1.0 1.0 95 | ref_t = 310 310 96 | 97 | gen_vel = no 98 | gen_temp = 310 99 | gen_seed = 473529 100 | 101 | Pcoupl = berendsen 102 | Pcoupltype = semiisotropic 103 | tau_p = 3.0 104 | compressibility = 3e-4 3e-4 105 | ref_p = 1.0 1.0 106 | refcoord-scaling = all 107 | 108 | ; Center of mass removal 109 | comm-mode = Linear 110 | nstcomm = 100 111 | comm-grps = Rest Solvent 112 | 113 | ; MARTINI and CONSTRAINTS 114 | ; for ring systems and stiff bonds constraints are defined 115 | ; which are best handled using Lincs. 116 | 117 | constraints = none 118 | constraint_algorithm = Lincs 119 | lincs_order = 8 120 | lincs_warnangle = 90 121 | lincs_iter = 2 122 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-eq3.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | title = Martini 10 | 11 | ; TIMESTEP IN MARTINI 12 | ; Most simulations are numerically stable with dt=40 fs, 13 | ; however better energy conservation is achieved using a 14 | ; 20-30 fs timestep. 15 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 16 | 17 | ; define = -DFIX_UNDU -DPOSRES -DFLEXIBLE ; when hight field is added put undulations back in 18 | integrator = md 19 | dt = 0.01 20 | nsteps = 400000 21 | 22 | nstxout = 0 23 | nstvout = 0 24 | nstfout = 0 25 | nstlog = 25000 26 | nstenergy = 25000 27 | nstxout-compressed = 25000 28 | compressed-x-precision = 100 29 | compressed-x-grps = 30 | energygrps = System 31 | 32 | ; NEIGHBOURLIST and MARTINI 33 | ; To achieve faster simulations in combination with the Verlet-neighborlist 34 | ; scheme, Martini can be simulated with a straight cutoff. In order to 35 | ; do so, the cutoff distance is reduced 1.1 nm. 36 | ; Neighborlist length should be optimized depending on your hardware setup: 37 | ; updating ever 20 steps should be fine for classic systems, while updating 38 | ; every 30-40 steps might be better for GPU based systems. 39 | ; The Verlet neighborlist scheme will automatically choose a proper neighborlist 40 | ; length, based on a energy drift tolerance. 41 | ; 42 | ; Coulomb interactions can alternatively be treated using a reaction-field, 43 | ; giving slightly better properties. 44 | ; Please realize that electrostVatic interactions in the Martini model are 45 | ; not considered to be very accurate to begin with, especially as the 46 | ; screening in the system is set to be uniform across the system with 47 | ; a screening constant of 15. When using PME, please make sure your 48 | ; system properties are still reasonable. 49 | ; 50 | ; With the polarizable water model, the relative electrostatic screening 51 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 52 | ; apolar solvent. The polarizable water itself will perform the explicit screening 53 | ; in aqueous environment. In this case, the use of PME is more realistic. 54 | 55 | 56 | cutoff-scheme = Verlet 57 | nstlist = 20 58 | nsttcouple = 20 59 | nstpcouple = 20 60 | rlist = 1.35 61 | verlet-buffer-tolerance = -1 62 | ns_type = grid 63 | pbc = xyz 64 | 65 | coulombtype = reaction-field 66 | rcoulomb = 1.1 67 | epsilon_r = 15 ; 2.5 (with polarizable water) 68 | epsilon_rf = 0 69 | vdw_type = cutoff 70 | vdw-modifier = Potential-shift-verlet 71 | rvdw = 1.1 72 | 73 | ; MARTINI and TEMPERATURE/PRESSURE 74 | ; normal temperature and pressure coupling schemes can be used. 75 | ; It is recommended to couple individual groups in your system separately. 76 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 77 | ; thermostat using a coupling constant of the order of 1 ps. Even better 78 | ; temperature control can be achieved by reducing the temperature coupling 79 | ; constant to 0.1 ps, although with such tight coupling (approaching 80 | ; the time step) one can no longer speak of a weak-coupling scheme. 81 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 82 | ; The Berendsen thermostat is less suited since it does not give 83 | ; a well described thermodynamic ensemble. 84 | ; 85 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 86 | ; with a coupling constant in the range 4-8 ps and typical compressibility 87 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 88 | ; the Berendsen barostat probably gives better results, as the Parrinello- 89 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 90 | ; coupling should be done semiisotropic. 91 | 92 | tcoupl = berendsen 93 | tc-grps = Solvent Rest 94 | tau_t = 1.0 1.0 95 | ref_t = 310 310 96 | 97 | gen_vel = no 98 | gen_temp = 310 99 | gen_seed = 473529 100 | 101 | Pcoupl = berendsen 102 | Pcoupltype = semiisotropic 103 | tau_p = 3.0 104 | compressibility = 3e-4 3e-4 105 | ref_p = 1.0 1.0 106 | refcoord_scaling = all 107 | 108 | ; Center of mass removal 109 | comm-mode = Linear 110 | nstcomm = 100 111 | comm-grps = Rest Solvent 112 | 113 | ; MARTINI and CONSTRAINTS 114 | ; for ring systems and stiff bonds constraints are defined 115 | ; which are best handled using Lincs. 116 | 117 | constraints = none 118 | constraint_algorithm = Lincs 119 | lincs_order = 8 120 | lincs_warnangle = 90 121 | lincs_iter = 2 122 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-eq1.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | title = Martini 10 | 11 | ; TIMESTEP IN MARTINI 12 | ; Most simulations are numerically stable with dt=40 fs, 13 | ; however better energy conservation is achieved using a 14 | ; 20-30 fs timestep. 15 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 16 | 17 | ; define = -DFIX_UNDU -DPOSRES -DFLEXIBLE ; when hight field is added put undulations back in 18 | integrator = md 19 | dt = 0.001 20 | nsteps = 5000 21 | 22 | nstxout = 0 23 | nstvout = 0 24 | nstfout = 0 25 | nstlog = 25000 26 | nstenergy = 25000 27 | nstxout-compressed = 25000 28 | compressed-x-precision = 100 29 | compressed-x-grps = 30 | energygrps = System 31 | 32 | ; NEIGHBOURLIST and MARTINI 33 | ; To achieve faster simulations in combination with the Verlet-neighborlist 34 | ; scheme, Martini can be simulated with a straight cutoff. In order to 35 | ; do so, the cutoff distance is reduced 1.1 nm. 36 | ; Neighborlist length should be optimized depending on your hardware setup: 37 | ; updating ever 20 steps should be fine for classic systems, while updating 38 | ; every 30-40 steps might be better for GPU based systems. 39 | ; The Verlet neighborlist scheme will automatically choose a proper neighborlist 40 | ; length, based on a energy drift tolerance. 41 | ; 42 | ; Coulomb interactions can alternatively be treated using a reaction-field, 43 | ; giving slightly better properties. 44 | ; Please realize that electrostVatic interactions in the Martini model are 45 | ; not considered to be very accurate to begin with, especially as the 46 | ; screening in the system is set to be uniform across the system with 47 | ; a screening constant of 15. When using PME, please make sure your 48 | ; system properties are still reasonable. 49 | ; 50 | ; With the polarizable water model, the relative electrostatic screening 51 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 52 | ; apolar solvent. The polarizable water itself will perform the explicit screening 53 | ; in aqueous environment. In this case, the use of PME is more realistic. 54 | 55 | 56 | cutoff-scheme = Verlet 57 | nstlist = 20 58 | nsttcouple = 20 59 | nstpcouple = 20 60 | rlist = 1.35 61 | verlet-buffer-tolerance = -1 62 | ns_type = grid 63 | pbc = xyz 64 | 65 | coulombtype = reaction-field 66 | rcoulomb = 1.1 67 | epsilon_r = 15 ; 2.5 (with polarizable water) 68 | epsilon_rf = 0 69 | vdw_type = cutoff 70 | vdw-modifier = Potential-shift-verlet 71 | rvdw = 1.1 72 | 73 | ; MARTINI and TEMPERATURE/PRESSURE 74 | ; normal temperature and pressure coupling schemes can be used. 75 | ; It is recommended to couple individual groups in your system separately. 76 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 77 | ; thermostat using a coupling constant of the order of 1 ps. Even better 78 | ; temperature control can be achieved by reducing the temperature coupling 79 | ; constant to 0.1 ps, although with such tight coupling (approaching 80 | ; the time step) one can no longer speak of a weak-coupling scheme. 81 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 82 | ; The Berendsen thermostat is less suited since it does not give 83 | ; a well described thermodynamic ensemble. 84 | ; 85 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 86 | ; with a coupling constant in the range 4-8 ps and typical compressibility 87 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 88 | ; the Berendsen barostat probably gives better results, as the Parrinello- 89 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 90 | ; coupling should be done semiisotropic. 91 | 92 | tcoupl = berendsen 93 | tc-grps = Solvent Rest ; Maybe change these to x3 lipids solvent protein ? 94 | tau_t = 1.0 1.0 95 | ref_t = 310 310 96 | 97 | gen_vel = yes 98 | gen_temp = 320 99 | gen_seed = 473529 100 | 101 | Pcoupl = berendsen 102 | Pcoupltype = semiisotropic 103 | tau_p = 10.0 104 | compressibility = 3e-4 3e-4 105 | ref_p = 1.0 1.0 106 | refcoord-scaling = all 107 | 108 | ; Center of mass removal 109 | comm-mode = Linear 110 | nstcomm = 100 111 | comm-grps = Rest Solvent 112 | 113 | ; MARTINI and CONSTRAINTS 114 | ; for ring systems and stiff bonds constraints are defined 115 | ; which are best handled using Lincs. 116 | 117 | constraints = none 118 | constraint_algorithm = Lincs 119 | lincs_order = 8 120 | lincs_warnangle = 90 121 | lincs_iter = 2 122 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_phospholipids_CL_v2.itp: -------------------------------------------------------------------------------- 1 | ; Cardiolipin (CL) 2- 2 | ; 3 | ; Please cite: 4 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 5 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 6 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 7 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 8 | ; 9 | ; Last updated: Dec-2024 by Kasper 10 | ; Authors: Kasper B. Pedersen 11 | ; 12 | 13 | ;;;;; 14 | ;;;;; Tetramyristyoyl cardiolipin 15 | ;;;;; TMCL 16 | ;;;;; 17 | 18 | [ moleculetype ] 19 | ; molname nrexcl 20 | TMCL 1 21 | 22 | [ atoms ] 23 | ; i type resnr residue atom cgnr charge 24 | 1 N6 1 TMCL GLC 1 0.0 ; linking bead 25 | 2 Q5 1 TMCL PO41 2 -1.0 ; first phosphatidyl group 26 | 3 SN4a 1 TMCL GL11 3 0.0 ; first glycerol group 27 | 4 SN4a 1 TMCL GL21 4 0.0 28 | 5 C1 1 TMCL C1A1 5 0.0 ; aliphatic tail A1 29 | 6 C1 1 TMCL C2A1 6 0.0 30 | 7 C1 1 TMCL C3A1 7 0.0 31 | 8 C1 1 TMCL C1B1 10 0.0 ; aliphatic tail B1 32 | 9 C1 1 TMCL C2B1 11 0.0 33 | 10 C1 1 TMCL C3B1 12 0.0 34 | 11 Q5 1 TMCL PO42 15 -1.0 ; second phosphatidyl group 35 | 12 SN4a 1 TMCL GL12 16 0.0 ; second glycerol group 36 | 13 SN4a 1 TMCL GL22 17 0.0 37 | 14 C1 1 TMCL C1A2 18 0.0 ; aliphatic tail A2 38 | 15 C1 1 TMCL C2A2 19 0.0 39 | 16 C1 1 TMCL C3A2 20 0.0 40 | 17 C1 1 TMCL C1B2 23 0.0 ; aliphatic tail B2 41 | 18 C1 1 TMCL C2B2 24 0.0 42 | 19 C1 1 TMCL C3B2 25 0.0 43 | 44 | [ bonds ] 45 | ; i j 46 | 1 2 b_PO4_GL_cl 47 | 1 11 b_PO4_GL_cl 48 | 2 3 b_PO4_GL_def 49 | 2 4 b_PO4_GL_def_long 50 | 3 4 b_GL_GL_glyc 51 | 3 5 b_GL_C1_glyc_5long 52 | 5 6 b_C1_C1_mid_5long 53 | 6 7 b_C1_C1_end 54 | 4 8 b_GL_C1_glyc_5long 55 | 8 9 b_C1_C1_mid_5long 56 | 9 10 b_C1_C1_end 57 | 11 12 b_PO4_GL_def 58 | 11 13 b_PO4_GL_def_long 59 | 12 13 b_GL_GL_glyc 60 | 12 14 b_GL_C1_glyc_5long 61 | 14 15 b_C1_C1_mid_5long 62 | 15 16 b_C1_C1_end 63 | 13 17 b_GL_C1_glyc_5long 64 | 17 18 b_C1_C1_mid_5long 65 | 18 19 b_C1_C1_end 66 | 67 | [ angles ] 68 | ; i j k 69 | 2 1 11 a_PO4_GL_PO4_cl 70 | 1 2 3 a_GL_PO4_GL_cl 71 | 1 11 12 a_GL_PO4_GL_cl 72 | 2 3 5 a_PO4_GL_C_def 73 | 4 3 5 a_GL_GL_C_glyc 74 | 3 4 8 a_GL_GL_C_glyc 75 | 3 5 6 a_GL_C1_C1_glyc 76 | 5 6 7 a_C1_C1_C1_def 77 | 4 8 9 a_GL_C1_C1_glyc 78 | 8 9 10 a_C1_C1_C1_def 79 | 11 12 14 a_PO4_GL_C_def 80 | 13 12 14 a_GL_GL_C_glyc 81 | 12 13 17 a_GL_GL_C_glyc 82 | 12 14 15 a_GL_C1_C1_glyc 83 | 14 15 16 a_C1_C1_C1_def 84 | 13 17 18 a_GL_C1_C1_glyc 85 | 17 18 19 a_C1_C1_C1_def 86 | 87 | ;;;;; 88 | ;;;;; Tetraoleoyl cardiolipin 89 | ;;;;; TOCL 90 | ;;;;; 91 | 92 | [ moleculetype ] 93 | ; molname nrexcl 94 | TOCL 1 95 | 96 | [ atoms ] 97 | ; i type resnr residue atom cgnr charge 98 | 1 N6 1 TOCL GLC 1 0.0 ; linking bead 99 | 2 Q5 1 TOCL PO41 2 -1.0 ; first phosphatidyl group 100 | 3 SN4a 1 TOCL GL11 3 0.0 ; first glycerol group 101 | 4 SN4a 1 TOCL GL21 4 0.0 102 | 5 C1 1 TOCL C1A1 5 0.0 ; aliphatic tail A1 103 | 6 C4h 1 TOCL D2A1 6 0.0 104 | 7 C1 1 TOCL C3A1 7 0.0 105 | 8 C1 1 TOCL C4A1 8 0.0 106 | 9 C1 1 TOCL C1B1 10 0.0 ; aliphatic tail B1 107 | 10 C4h 1 TOCL D2B1 11 0.0 108 | 11 C1 1 TOCL C3B1 12 0.0 109 | 12 C1 1 TOCL C4B1 13 0.0 110 | 13 Q5 1 TOCL PO42 15 -1.0 ; second phosphatidyl group 111 | 14 SN4a 1 TOCL GL12 16 0.0 ; second glycerol group 112 | 15 SN4a 1 TOCL GL22 17 0.0 113 | 16 C1 1 TOCL C1A2 18 0.0 ; aliphatic tail A2 114 | 17 C4h 1 TOCL D2A2 19 0.0 115 | 18 C1 1 TOCL C3A2 20 0.0 116 | 19 C1 1 TOCL C4A2 21 0.0 117 | 20 C1 1 TOCL C1B2 23 0.0 ; aliphatic tail B2 118 | 21 C4h 1 TOCL D2B2 24 0.0 119 | 22 C1 1 TOCL C3B2 25 0.0 120 | 23 C1 1 TOCL C4B2 26 0.0 121 | 122 | [ bonds ] 123 | ; i j 124 | 1 2 b_PO4_GL_cl 125 | 1 13 b_PO4_GL_cl 126 | 2 3 b_PO4_GL_def 127 | 2 4 b_PO4_GL_def_long 128 | 3 4 b_GL_GL_glyc 129 | 3 5 b_GL_C1_glyc_5long 130 | 5 6 b_C1_C4_mid_5long 131 | 6 7 b_C4_C1_mid 132 | 7 8 b_C1_C1_end 133 | 4 9 b_GL_C1_glyc_5long 134 | 9 10 b_C1_C4_mid_5long 135 | 10 11 b_C4_C1_mid 136 | 11 12 b_C1_C1_end 137 | 13 14 b_PO4_GL_def 138 | 13 15 b_PO4_GL_def_long 139 | 14 15 b_GL_GL_glyc 140 | 14 16 b_GL_C1_glyc_5long 141 | 16 17 b_C1_C4_mid_5long 142 | 17 18 b_C4_C1_mid 143 | 18 19 b_C1_C1_end 144 | 15 20 b_GL_C1_glyc_5long 145 | 20 21 b_C1_C4_mid_5long 146 | 21 22 b_C4_C1_mid 147 | 22 23 b_C1_C1_end 148 | 149 | [ angles ] 150 | ; i j k 151 | 2 1 13 a_PO4_GL_PO4_cl 152 | 1 2 3 a_GL_PO4_GL_cl 153 | 1 13 14 a_GL_PO4_GL_cl 154 | 2 3 5 a_PO4_GL_C_def 155 | 4 3 5 a_GL_GL_C_glyc 156 | 3 4 9 a_GL_GL_C_glyc 157 | 3 5 6 a_GL_C1_C4_glyc 158 | 5 6 7 a_C1_C4_C1_def 159 | 6 7 8 a_C4_C1_C1_def 160 | 4 9 10 a_GL_C1_C4_glyc 161 | 9 10 11 a_C1_C4_C1_def 162 | 10 11 12 a_C4_C1_C1_def 163 | 13 14 16 a_PO4_GL_C_def 164 | 15 14 16 a_GL_GL_C_glyc 165 | 14 15 20 a_GL_GL_C_glyc 166 | 14 16 17 a_GL_C1_C4_glyc 167 | 16 17 18 a_C1_C4_C1_def 168 | 17 18 19 a_C4_C1_C1_def 169 | 15 20 21 a_GL_C1_C4_glyc 170 | 20 21 22 a_C1_C4_C1_def 171 | 21 22 23 a_C4_C1_C1_def 172 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/martini_benchmark_dhh.csv: -------------------------------------------------------------------------------- 1 | Ref Name,Lipid Tail,DHH [nm],Uncertainty [nm],T [K],NaCl [M],Ref 2 | DLPC,12:0/12:0,3,0.06,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 3 | DLPC,12:0/12:0,2.96,0.06,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 4 | DLPC,12:0/12:0,2.96,0.06,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 5 | DLPC,12:0/12:0,2.96,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 6 | ,,,,,, 7 | DMPC,14:0/14:0,3.45,0.07,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 8 | DMPC,14:0/14:0,3.22,0.07,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 9 | DMPC,14:0/14:0,3.22,0.07,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 10 | ,,,,,, 11 | DPPC,16:0/16:0,3.86,0.08,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 12 | DPPC,16:0/16:0,3.46,0.07,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 13 | ,,,,,, 14 | DSPC,18:0/18:0,4.33,0.09,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 15 | ,,,,,, 16 | MSPC,14:0/18:0,3.57,0.07,323.15,no,https://doi.org/10.3390/sym13081441 17 | SMPC,18:0/14:0,3.48,0.07,323.15,no,https://doi.org/10.3390/sym13081441 18 | PMPC,16:0/14:0,3.39,0.07,323.15,no,https://doi.org/10.3390/sym13081441 19 | ,,,,,, 20 | DRPC,14:1/14:1,2.96,0.06,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 21 | DYPC,16:1/16:1,3.21,0.06,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 22 | DOPC,18:1/18:1,3.7,0.07,293.15,no,https://doi.org/10.1039/C6SM02727J 23 | DOPC,18:1/18:1,3.68,0.07,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 24 | DGPC,20:1/20:1,3.89,0.08,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 25 | DEPC,22:1/22:1,4.55,0.09,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 26 | DNPC,24:1/24:1,4.79,0.1,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 27 | ,,,,,, 28 | PSM,d18:1/16:0,3.89,0.08,318.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 29 | PSM,d18:1/16:0,3.78,0.08,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 30 | SSM,d18:1/18:0,4,0.08,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 31 | SSM,d18:1/18:0,3.94,0.08,338.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 32 | ,,,,,, 33 | POPC,16:0/18:1,3.74,0.07,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 34 | POPC,16:0/18:1,3.65,0.07,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 35 | POPC,16:0/18:1,3.6,0.07,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 36 | POPC,16:0/18:1,3.59,0.07,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 37 | ,,,,,, 38 | SOPC,18:0/18:1,3.85,0.08,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 39 | SOPC,18:0/18:1,3.86,0.08,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 40 | SOPC,18:0/18:1,3.7,0.07,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 41 | SOPC,18:0/18:1,3.58,0.07,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 42 | ,,,,,, 43 | PDPC,16:0/22:6,3.32,0.07,293.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 44 | PDPC,16:0/22:6,3.3,0.07,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 45 | PDPC,16:0/22:6,3.22,0.06,313.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 46 | ,,,,,, 47 | SDPC,18:0/22:6,3.52,0.07,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 48 | ,,,,,, 49 | DLPE,12:0/12:0,3.35,0.07,308.15,no,https://doi.org/10.1021/jp511159q 50 | DLPE,12:0/12:0,3.25,0.07,318.15,no,https://doi.org/10.1021/jp511159q 51 | DLPE,12:0/12:0,3.15,0.06,328.15,no,https://doi.org/10.1021/jp511159q 52 | ,,,,,, 53 | POPE,16:0/18:1,3.83,0.08,308.15,no,https://doi.org/10.1021/jp511159q 54 | POPE,16:0/18:1,3.74,0.07,313.15,no,https://doi.org/10.1021/jp511159q 55 | POPE,16:0/18:1,3.87,0.08,323.15,no,https://doi.org/10.1021/jp511159q 56 | ,,,,,, 57 | SOPE,18:0/18:1,4.16,0.08,308.15,no,https://doi.org/10.1021/jp511159q 58 | SOPE,18:0/18:1,4.01,0.08,313.15,no,https://doi.org/10.1021/jp511159q 59 | SOPE,18:0/18:1,3.98,0.08,323.15,no,https://doi.org/10.1021/jp511159q 60 | ,,,,,, 61 | DLPG,12:0/12:0,3,0.06,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 62 | DLPG,12:0/12:0,2.94,0.06,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 63 | DLPG,12:0/12:0,2.88,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 64 | DLPG,12:0/12:0,2.84,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 65 | ,,,,,, 66 | DMPG,14:0/14:0,3.46,0.07,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 67 | DMPG,14:0/14:0,3.46,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 68 | DMPG,14:0/14:0,3.38,0.07,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 69 | ,,,,,, 70 | DPPG,16:0/16:0,3.86,0.08,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 71 | DPPG,16:0/16:0,3.76,0.08,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 72 | ,,,,,, 73 | DSPG,18:0/18:0,4.12,0.08,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 74 | ,,,,,, 75 | POPG,16:0/18:1,3.7,0.07,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 76 | POPG,16:0/18:1,3.66,0.07,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 77 | POPG,16:0/18:1,3.56,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 78 | POPG,16:0/18:1,3.54,0.07,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 79 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| Ref Name,Lipid Tail,DB [nm],Uncertainty [nm],T [K],NaCl [M],Ref 2 | DLPC,12:0/12:0,3.3,0.07,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 3 | DLPC,12:0/12:0,3.26,0.07,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 4 | DLPC,12:0/12:0,3.1,0.06,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 5 | DLPC,12:0/12:0,3.07,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 6 | ,,,,,, 7 | DMPC,14:0/14:0,3.67,0.07,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 8 | DMPC,14:0/14:0,3.52,0.07,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 9 | DMPC,14:0/14:0,3.42,0.07,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 10 | ,,,,,, 11 | DPPC,16:0/16:0,3.9,0.08,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 12 | DPPC,16:0/16:0,3.81,0.08,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 13 | ,,,,,, 14 | DSPC,18:0/18:0,4.22,0.08,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 15 | ,,,,,, 16 | MSPC,14:0/18:0,4.03,0.08,323.15,no,https://doi.org/10.3390/sym13081441 17 | SMPC,18:0/14:0,4.03,0.08,323.15,no,https://doi.org/10.3390/sym13081441 18 | PMPC,16:0/14:0,3.84,0.08,323.15,no,https://doi.org/10.3390/sym13081441 19 | ,,,,,, 20 | DRPC,14:1/14:1,3.37,0.07,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 21 | DYPC,16:1/16:1,3.62,0.07,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 22 | DOPC,18:1/18:1,3.94,0.08,293.15,no,https://doi.org/10.1039/C6SM02727J 23 | DOPC,18:1/18:1,3.89,0.08,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 24 | DGPC,20:1/20:1,4.25,0.09,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 25 | DEPC,22:1/22:1,4.64,0.09,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 26 | DNPC,24:1/24:1,5.22,0.1,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050 27 | ,,,,,, 28 | PSM,d18:1/16:0,3.84,0.08,318.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 29 | PSM,d18:1/16:0,3.75,0.08,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 30 | SSM,d18:1/18:0,3.93,0.08,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 31 | SSM,d18:1/18:0,3.81,0.08,338.15,no,https://doi.org/10.1021/acs.jpcb.0c03389 32 | ,,,,,, 33 | POPC,16:0/18:1,3.98,0.08,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 34 | POPC,16:0/18:1,3.91,0.08,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 35 | POPC,16:0/18:1,3.79,0.08,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 36 | POPC,16:0/18:1,3.77,0.08,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 37 | ,,,,,, 38 | SOPC,18:0/18:1,4.08,0.08,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 39 | SOPC,18:0/18:1,4,0.08,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 40 | SOPC,18:0/18:1,3.9,0.08,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 41 | SOPC,18:0/18:1,3.85,0.08,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022 42 | ,,,,,, 43 | PDPC,16:0/22:6,3.74,0.07,293.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 44 | PDPC,16:0/22:6,3.68,0.07,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 45 | PDPC,16:0/22:6,3.61,0.07,313.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 46 | ,,,,,, 47 | SDPC,18:0/22:6,3.88,0.08,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892 48 | ,,,,,, 49 | DLPE,12:0/12:0,3.49,0.07,308.15,no,https://doi.org/10.1021/jp511159q 50 | DLPE,12:0/12:0,3.38,0.07,318.15,no,https://doi.org/10.1021/jp511159q 51 | DLPE,12:0/12:0,3.29,0.07,328.15,no,https://doi.org/10.1021/jp511159q 52 | ,,,,,, 53 | POPE,16:0/18:1,4.05,0.08,308.15,no,https://doi.org/10.1021/jp511159q 54 | POPE,16:0/18:1,3.99,0.08,313.15,no,https://doi.org/10.1021/jp511159q 55 | POPE,16:0/18:1,3.88,0.08,323.15,no,https://doi.org/10.1021/jp511159q 56 | ,,,,,, 57 | SOPE,18:0/18:1,4.31,0.09,308.15,no,https://doi.org/10.1021/jp511159q 58 | SOPE,18:0/18:1,4.26,0.09,313.15,no,https://doi.org/10.1021/jp511159q 59 | SOPE,18:0/18:1,4.13,0.08,323.15,no,https://doi.org/10.1021/jp511159q 60 | ,,,,,, 61 | DLPG,12:0/12:0,3.14,0.06,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 62 | DLPG,12:0/12:0,3.07,0.06,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 63 | DLPG,12:0/12:0,2.95,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 64 | DLPG,12:0/12:0,2.89,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 65 | ,,,,,, 66 | DMPG,14:0/14:0,3.38,0.07,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 67 | DMPG,14:0/14:0,3.26,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 68 | DMPG,14:0/14:0,3.2,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 69 | ,,,,,, 70 | DPPG,16:0/16:0,3.67,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 71 | DPPG,16:0/16:0,3.59,0.07,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 72 | ,,,,,, 73 | DSPG,18:0/18:0,3.91,0.08,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 74 | ,,,,,, 75 | POPG,16:0/18:1,3.85,0.08,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 76 | POPG,16:0/18:1,3.76,0.08,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 77 | POPG,16:0/18:1,3.61,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 78 | POPG,16:0/18:1,3.57,0.07,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 79 | ,,,,,, 80 | SOPG,18:0/18:1,4.02,0.08,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 81 | SOPG,18:0/18:1,3.96,0.08,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 82 | SOPG,18:0/18:1,3.81,0.08,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 83 | SOPG,18:0/18:1,3.76,0.08,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 84 | ,,,,,, 85 | DOPG,18:1/18:1,3.71,0.07,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 86 | DOPG,18:1/18:1,3.66,0.07,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 87 | DOPG,18:1/18:1,3.6,0.07,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 88 | DOPG,18:1/18:1,3.59,0.07,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009 89 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/martini_benchmark_2dc.csv: -------------------------------------------------------------------------------- 1 | Ref Name,Lipid Tail,2Dc [nm],Uncertainty [nm],T [K],NaCl [M],Ref,, 2 | DLPC,12:0/12:0,2.19,0.04,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 3 | DLPC,12:0/12:0,2.17,0.04,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 4 | DLPC,12:0/12:0,2.08,0.04,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 5 | DLPC,12:0/12:0,2.06,0.04,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 6 | ,,,,,,,, 7 | DMPC,14:0/14:0,2.57,0.05,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 8 | DMPC,14:0/14:0,2.48,0.05,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 9 | DMPC,14:0/14:0,2.41,0.05,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 10 | ,,,,,,,, 11 | DPPC,16:0/16:0,2.85,0.06,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 12 | DPPC,16:0/16:0,2.79,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 13 | ,,,,,,,, 14 | DSPC,18:0/18:0,3.19,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 15 | ,,,,,,,, 16 | MSPC,14:0/18:0,2.91,0.06,323.15,no,https://doi.org/10.3390/sym13081441,, 17 | SMPC,18:0/14:0,2.92,0.06,323.15,no,https://doi.org/10.3390/sym13081441,, 18 | PMPC,16:0/14:0,2.7,0.05,323.15,no,https://doi.org/10.3390/sym13081441,, 19 | ,,,,,,,, 20 | DRPC,14:1/14:1,2.34,0.05,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 21 | DYPC,16:1/16:1,2.62,0.05,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 22 | DOPC,18:1/18:1,3,0.06,293.15,no,https://doi.org/10.1039/C6SM02727J,, 23 | DOPC,18:1/18:1,2.9,0.06,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 24 | DGPC,20:1/20:1,3.26,0.07,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 25 | DEPC,22:1/22:1,3.64,0.07,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 26 | DNPC,24:1/24:1,4.08,0.08,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 27 | ,,,,,,,, 28 | PSM,d18:1/16:0,2.93,0.06,318.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 29 | PSM,d18:1/16:0,2.87,0.06,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 30 | SSM,d18:1/18:0,3.05,0.06,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 31 | SSM,d18:1/18:0,2.97,0.06,338.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 32 | ,,,,,,,, 33 | POPC,16:0/18:1,2.92,0.06,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 34 | POPC,16:0/18:1,2.88,0.06,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 35 | POPC,16:0/18:1,2.81,0.06,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 36 | POPC,16:0/18:1,2.8,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 37 | ,,,,,,,, 38 | SOPC,18:0/18:1,3.04,0.06,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 39 | SOPC,18:0/18:1,2.99,0.06,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 40 | SOPC,18:0/18:1,2.93,0.06,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 41 | SOPC,18:0/18:1,2.9,0.06,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 42 | ,,,,,,,, 43 | PDPC,16:0/22:6,2.82,0.06,293.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 44 | PDPC,16:0/22:6,2.78,0.06,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 45 | PDPC,16:0/22:6,2.73,0.05,313.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 46 | ,,,,,,,, 47 | SDPC,18:0/22:6,2.97,0.06,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 48 | ,,,,,,,, 49 | DLPE,12:0/12:0,2.54,0.05,308.15,no,https://doi.org/10.1021/jp511159q,, 50 | DLPE,12:0/12:0,2.47,0.05,318.15,no,https://doi.org/10.1021/jp511159q,, 51 | DLPE,12:0/12:0,2.41,0.05,328.15,no,https://doi.org/10.1021/jp511159q,, 52 | ,,,,,,,, 53 | POPE,16:0/18:1,3.21,0.06,308.15,no,https://doi.org/10.1021/jp511159q,, 54 | POPE,16:0/18:1,3.16,0.06,313.15,no,https://doi.org/10.1021/jp511159q,, 55 | POPE,16:0/18:1,3.08,0.06,323.15,no,https://doi.org/10.1021/jp511159q,, 56 | ,,,,,,,, 57 | SOPE,18:0/18:1,3.45,0.07,308.15,no,https://doi.org/10.1021/jp511159q,, 58 | SOPE,18:0/18:1,3.41,0.07,313.15,no,https://doi.org/10.1021/jp511159q,, 59 | SOPE,18:0/18:1,3.32,0.07,323.15,no,https://doi.org/10.1021/jp511159q,, 60 | ,,,,,,,, 61 | DLPG,12:0/12:0,2.17,0.04,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 62 | DLPG,12:0/12:0,2.13,0.04,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 63 | DLPG,12:0/12:0,2.06,0.04,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 64 | DLPG,12:0/12:0,2.03,0.04,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 65 | ,,,,,,,, 66 | DMPG,14:0/14:0,2.45,0.05,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 67 | DMPG,14:0/14:0,2.37,0.05,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 68 | DMPG,14:0/14:0,2.34,0.05,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 69 | ,,,,,,,, 70 | DPPG,16:0/16:0,2.77,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 71 | DPPG,16:0/16:0,2.72,0.05,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 72 | ,,,,,,,, 73 | DSPG,18:0/18:0,3.04,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 74 | ,,,,,,,, 75 | POPG,16:0/18:1,2.91,0.06,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 76 | POPG,16:0/18:1,2.85,0.06,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 77 | POPG,16:0/18:1,2.76,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 78 | POPG,16:0/18:1,2.74,0.05,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 79 | ,,,,,,,, 80 | SOPG,18:0/18:1,3.1,0.06,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 81 | SOPG,18:0/18:1,3.05,0.06,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 82 | SOPG,18:0/18:1,2.95,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 83 | SOPG,18:0/18:1,2.92,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 84 | ,,,,,,,, 85 | DOPG,18:1/18:1,2.85,0.06,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 86 | DOPG,18:1/18:1,2.82,0.06,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 87 | DOPG,18:1/18:1,2.79,0.06,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 88 | DOPG,18:1/18:1,2.78,0.06,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 89 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_monoglycerides_v2.itp: -------------------------------------------------------------------------------- 1 | 2 | ;;;;; MARTINI 3.0 - Monoglycerides 3 | ;;;;; 4 | 5 | ; please cite: 6 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 7 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 8 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 9 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 10 | ; last edit Jan-2025, Kasper 11 | 12 | ;;;;; 13 | ;;;;; Monoolein 14 | ;;;;; MO 15 | ;;;;; 16 | 17 | ;;;;; BEAD-INDEX MAPPING 18 | ;;;;; topology description 19 | ; 20 | ; DOH-GL1-C1A-D2A-C3A-C4A 1-2-3-4-5-6 21 | ; 22 | 23 | [moleculetype] 24 | MO 1 25 | 26 | [atoms] 27 | ; id type resnr residu atom cgnr charge 28 | 1 SP4r 1 MO DOH 1 0 29 | 2 SN4a 1 MO GL1 2 0 30 | 3 C1 1 MO C1A 3 0 ; 5-1 mapping 31 | 4 C4h 1 MO D2A 4 0 32 | 5 C1 1 MO C3A 5 0 33 | 6 C1 1 MO C4A 6 0 34 | 35 | [bonds] 36 | ; i j funct length force.c. 37 | 1 2 b_DOH_GL_def 38 | 2 3 b_GL_C1_glyc_5long 39 | 3 4 b_C1_C4_mid_5long 40 | 4 5 b_C1_C4_mid 41 | 5 6 b_C1_C1_end 42 | 43 | [angles] 44 | 1 2 3 a_DOH_GL_C_def 45 | 2 3 4 a_GL_C1_C4_glyc 46 | 3 4 5 a_C1_C4_C1_def 47 | 4 5 6 a_C1_C1_C4_def 48 | 49 | ;;;;; 50 | ;;;;; Monolinoolein 51 | ;;;;; ML 52 | ;;;;; 53 | 54 | ;;;;; BEAD-INDEX MAPPING 55 | ;;;;; topology description 56 | ; 57 | ; DOH-GL1-C1A-D2A-D3A-C4A 1-2-3-4-5-6 58 | ; 59 | 60 | [moleculetype] 61 | ML 1 62 | 63 | [atoms] 64 | ; id type resnr residu atom cgnr charge 65 | 1 SP4r 1 ML DOH 1 0 66 | 2 SN4a 1 ML GL1 2 0 67 | 3 C1 1 ML C1A 3 0 ; 5-1 mapping 68 | 4 C4h 1 ML D2A 4 0 69 | 5 C4h 1 ML D3A 5 0 70 | 6 C1 1 ML C4A 6 0 71 | 72 | [bonds] 73 | ; i j funct length force.c. 74 | 1 2 b_DOH_GL_def 75 | 2 3 b_GL_C1_glyc_5long 76 | 3 4 b_C1_C4_mid_5long 77 | 4 5 b_C4_C4_mid 78 | 5 6 b_C1_C4_mid 79 | 80 | [angles] 81 | 1 2 3 a_DOH_GL_C_def 82 | 2 3 4 a_GL_C1_C4_glyc 83 | 3 4 5 a_C1_C4_C4_def 84 | 4 5 6 a_C1_C4_C4_def 85 | 86 | ;;;;; 87 | ;;;;; Monolinoolenin 88 | ;;;;; MLN 89 | ;;;;; 90 | 91 | ;;;;; BEAD-INDEX MAPPING 92 | ;;;;; topology description 93 | ; 94 | ; DOH-GL1-C1A-D2A-D3A-D4A 1-2-3-4-5-6 95 | ; 96 | 97 | [moleculetype] 98 | MLN 1 99 | 100 | [atoms] 101 | ; id type resnr residu atom cgnr charge 102 | 1 SP4r 1 MLN DOH 1 0 103 | 2 SN4a 1 MLN GL1 2 0 104 | 3 C1 1 MLN C1A 3 0 ; 5-1 mapping 105 | 4 C4h 1 MLN D2A 4 0 106 | 5 C4h 1 MLN D3A 5 0 107 | 6 C4h 1 MLN D4A 6 0 108 | 109 | [bonds] 110 | ; i j funct length force.c. 111 | 1 2 b_DOH_GL_def 112 | 2 3 b_GL_C1_glyc_5long 113 | 3 4 b_C1_C4_mid_5long 114 | 4 5 b_C4_C4_mid 115 | 5 6 b_C4_C4_mid 116 | 117 | [angles] 118 | 1 2 3 a_DOH_GL_C_def 119 | 2 3 4 a_GL_C1_C4_glyc 120 | 3 4 5 a_C1_C4_C4_def 121 | 4 5 6 a_C4_C4_C4_def 122 | 123 | ;;;;; Monostearin 124 | ;;;;; MS 125 | ;;;;; 126 | 127 | ;;;;; BEAD-INDEX MAPPING 128 | ;;;;; topology description 129 | ; 130 | ; DOH-GL1-C1A-C2A-C3A-C4A 1-2-3-4-5-6 131 | ; 132 | 133 | [moleculetype] 134 | MS 1 135 | 136 | [atoms] 137 | ; id type resnr residu atom cgnr charge 138 | 1 SP4r 1 MS DOH 1 0 139 | 2 SN4a 1 MS GL1 2 0 140 | 3 C1 1 MS C1A 3 0 ; 5-1 mapping 141 | 4 C1 1 MS C2A 4 0 142 | 5 C1 1 MS C3A 5 0 143 | 6 C1 1 MS C4A 6 0 144 | 145 | [bonds] 146 | ; i j funct length force.c. 147 | 1 2 b_DOH_GL_def 148 | 2 3 b_GL_C1_glyc_5long 149 | 3 4 b_C1_C1_mid_5long 150 | 4 5 b_C1_C1_mid 151 | 5 6 b_C1_C1_end 152 | 153 | [angles] 154 | 1 2 3 a_DOH_GL_C_def 155 | 2 3 4 a_GL_C1_C1_glyc 156 | 3 4 5 a_C1_C1_C1_def 157 | 4 5 6 a_C1_C1_C1_def 158 | 159 | ;;;;; Monoplamitin 160 | ;;;;; MP 161 | ;;;;; 162 | 163 | ;;;;; BEAD-INDEX MAPPING 164 | ;;;;; topology description 165 | ; 166 | ; DOH-GL1-C1A-C2A-C3A-C4A 1-2-3-4-5-6 167 | ; 168 | 169 | [moleculetype] 170 | MP 1 171 | 172 | [atoms] 173 | ; id type resnr residu atom cgnr charge 174 | 1 SP4r 1 MP DOH 1 0 175 | 2 SN4a 1 MP GL1 2 0 176 | 3 SC1 1 MP C1A 3 0 177 | 4 C1 1 MP C2A 4 0 178 | 5 C1 1 MP C3A 5 0 179 | 6 C1 1 MP C4A 6 0 180 | 181 | [bonds] 182 | ; i j funct length force.c. 183 | 1 2 b_DOH_GL_def 184 | 2 3 b_GL_SC1_glyc 185 | 3 4 b_SC1_C1_mid 186 | 4 5 b_C1_C1_mid 187 | 5 6 b_C1_C1_end 188 | 189 | [angles] 190 | 1 2 3 a_DOH_GL_C_def 191 | 2 3 4 a_GL_C1_C1_glyc 192 | 3 4 5 a_C1_C1_C1_def 193 | 4 5 6 a_C1_C1_C1_def 194 | 195 | ;;;;; Monomyristin 196 | ;;;;; MM 197 | ;;;;; 198 | 199 | ;;;;; BEAD-INDEX MAPPING 200 | ;;;;; topology description 201 | ; 202 | ; DOH-GL1-C1A-C2A-C3A 1-2-3-4-5 203 | ; 204 | 205 | [moleculetype] 206 | MM 1 207 | 208 | [atoms] 209 | ; id type resnr residu atom cgnr charge 210 | 1 SP4r 1 MM DOH 1 0 211 | 2 SN4a 1 MM GL1 2 0 212 | 3 C1 1 MM C1A 3 0 ; 5-1 mapping 213 | 4 C1 1 MM C2A 4 0 214 | 5 C1 1 MM C3A 5 0 215 | 216 | [bonds] 217 | ; i j funct length force.c. 218 | 1 2 b_DOH_GL_def 219 | 2 3 b_GL_C1_glyc_5long 220 | 3 4 b_C1_C1_mid_5long 221 | 4 5 b_C1_C1_end 222 | 223 | [angles] 224 | 1 2 3 a_DOH_GL_C_def 225 | 2 3 4 a_GL_C1_C1_glyc 226 | 3 4 5 a_C1_C1_C1_def 227 | 228 | ;;;;; Monolaurin 229 | ;;;;; MLA 230 | ;;;;; 231 | 232 | ;;;;; BEAD-INDEX MAPPING 233 | ;;;;; topology description 234 | ; 235 | ; DOH-GL1-C1A-C2A-C3A 1-2-3-4-5 236 | ; 237 | 238 | [moleculetype] 239 | MLA 1 240 | 241 | [atoms] 242 | ; id type resnr residu atom cgnr charge 243 | 1 SP4r 1 MLA DOH 1 0 244 | 2 SN4a 1 MLA GL1 2 0 245 | 3 SC1 1 MLA C1A 3 0 246 | 4 C1 1 MLA C2A 4 0 247 | 5 C1 1 MLA C3A 5 0 248 | 249 | [bonds] 250 | ; i j funct length force.c. 251 | 1 2 b_DOH_GL_def 252 | 2 3 b_GL_SC1_glyc 253 | 3 4 b_SC1_C1_mid 254 | 4 5 b_C1_C1_end 255 | 256 | [angles] 257 | 1 2 3 a_DOH_GL_C_def 258 | 2 3 4 a_GL_C1_C1_glyc 259 | 3 4 5 a_C1_C1_C1_def 260 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-eq4.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | ; TIMESTEP IN MARTINI 10 | ; Most simulations are numerically stable with dt=40 fs, 11 | ; however better energy conservation is achieved using a 12 | ; 20-30 fs timestep. 13 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 14 | 15 | ;define = -DPOS_Z_AXES -DFAR_Z_RES -DPOSRES -DPOSRES_FCX=10 -DPOSRES_FCY=10 -DPOSRES_FCZ=0 16 | integrator = md 17 | dt = 0.02 18 | nsteps = 100000 19 | 20 | nstxout = 0 21 | nstvout = 0 22 | nstfout = 0 23 | nstlog = 25000 24 | nstenergy = 25000 25 | nstxout-compressed = 25000 26 | compressed-x-precision = 100 27 | compressed-x-grps = 28 | energygrps = System 29 | 30 | ; NEIGHBOURLIST and MARTINI 31 | ; To achieve faster simulations in combination with the Verlet-neighborlist 32 | ; scheme, Martini can be simulated with a straight cutoff. In order to 33 | ; do so, the cutoff distance is reduced 1.1 nm. 34 | ; Neighborlist length should be optimized depending on your hardware setup: 35 | ; updating ever 20 steps should be fine for classic systems, while updating 36 | ; every 30-40 steps might be better for GPU based systems. 37 | ; The Verlet neighborlist scheme will automatically choose a proper neighborlist 38 | ; length, based on a energy drift tolerance. 39 | ; 40 | ; Coulomb interactions can alternatively be treated using a reaction-field, 41 | ; giving slightly better properties. 42 | ; Please realize that electrostVatic interactions in the Martini model are 43 | ; not considered to be very accurate to begin with, especially as the 44 | ; screening in the system is set to be uniform across the system with 45 | ; a screening constant of 15. When using PME, please make sure your 46 | ; system properties are still reasonable. 47 | ; 48 | ; With the polarizable water model, the relative electrostatic screening 49 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 50 | ; apolar solvent. The polarizable water itself will perform the explicit screening 51 | ; in aqueous environment. In this case, the use of PME is more realistic. 52 | 53 | cutoff-scheme = Verlet 54 | nstlist = 20 55 | nsttcouple = 20 56 | nstpcouple = 20 57 | rlist = 1.35 58 | verlet-buffer-tolerance = -1 59 | ns_type = grid 60 | pbc = xyz 61 | 62 | coulombtype = reaction-field 63 | rcoulomb = 1.1 64 | epsilon_r = 15 ; 2.5 (with polarizable water) 65 | epsilon_rf = 0 66 | vdw_type = cutoff 67 | vdw-modifier = Potential-shift-verlet 68 | rvdw = 1.1 69 | 70 | ; MARTINI and TEMPERATURE/PRESSURE 71 | ; normal temperature and pressure coupling schemes can be used. 72 | ; It is recommended to couple individual groups in your system separately. 73 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 74 | ; thermostat using a coupling constant of the order of 1 ps. Even better 75 | ; temperature control can be achieved by reducing the temperature coupling 76 | ; constant to 0.1 ps, although with such tight coupling (approaching 77 | ; the time step) one can no longer speak of a weak-coupling scheme. 78 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 79 | ; The Berendsen thermostat is less suited since it does not give 80 | ; a well described thermodynamic ensemble. 81 | ; 82 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 83 | ; with a coupling constant in the range 4-8 ps and typical compressibility 84 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 85 | ; the Berendsen barostat probably gives better results, as the Parrinello- 86 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 87 | ; coupling should be done semiisotropic. 88 | 89 | tcoupl = v-rescale 90 | tc-grps = Solvent Rest ; Maybe change these to x3 lipids solvent protein ? 91 | tau_t = 1.0 1.0 92 | ref_t = 310 310 93 | 94 | gen_vel = no 95 | gen_temp = 310 96 | gen_seed = 473529 97 | 98 | ; The recommended barostat is the stochastic cell rescaling barostat (c-rescale) 99 | ; due to its exponential relaxation property. Martini lipids are benchmarked 100 | ; with a coupling constant of 4 ps and compressibility 3e-4. 101 | ; C-rescale can be used for both equilibration and production simulations 102 | ; (https://doi.org/10.1063/5.0020514). 103 | ; For bilayer systems, the pressure should maintained using semiisotropic coupling. 104 | ; As of GROMACS 2023, c-rescale is not implemented for full anisotropic systems, 105 | ; but will likely be implemented (https://gitlab.com/gromacs/gromacs/-/merge_requests/3720). 106 | ; For now, full anisotropic coupling can be done using Berendsen barostat, even though 107 | ; the sampled ensemble is theoretically not NPT. The PR barostat is not recommended for 108 | ; crystal-like systems where crystal breaking (box elongation resulting in breaking) 109 | ; has been observed due to pressure oscillations. 110 | 111 | ; Pressure coupling 112 | Pcoupl = c-rescale 113 | Pcoupltype = semiisotropic 114 | tau_p = 4.0 115 | ref_p = 1.0 1.0 116 | compressibility = 3e-4 3e-4 117 | 118 | ; Center of mass removal 119 | comm-mode = Linear 120 | nstcomm = 100 121 | comm-grps = Rest Solvent 122 | 123 | ; MARTINI and CONSTRAINTS 124 | ; for ring systems and stiff bonds constraints are defined 125 | ; which are best handled using Lincs. 126 | 127 | constraints = none 128 | constraint_algorithm = Lincs 129 | lincs_order = 8 130 | lincs_warnangle = 90 131 | lincs_iter = 2 132 | -------------------------------------------------------------------------------- /tools/resources/martini_v3.0_prod.mdp: -------------------------------------------------------------------------------- 1 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 3.x 2 | ; Updated 20/12/2024 by Kasper B. Pedersen 3 | ; 4 | ; for use with GROMACS 5 5 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 6 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 7 | 8 | ; TIMESTEP IN MARTINI 9 | ; Most simulations are numerically stable with dt=40 fs, 10 | ; however better energy conservation is achieved using a 11 | ; 20-30 fs timestep. 12 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 13 | 14 | integrator = md 15 | dt = 0.02 16 | nsteps = 50000000 ; 1 us 17 | 18 | nstxout = 0 19 | nstvout = 0 20 | nstfout = 0 21 | nstlog = 25000 ; 0.5 ns 22 | nstenergy = 25000 ; 0.5 ns 23 | nstxout-compressed = 50000 ; 1 ns 24 | compressed-x-precision = 100 25 | compressed-x-grps = 26 | energygrps = System 27 | 28 | ; NEIGHBOURLIST and MARTINI 29 | ; To achieve faster simulations in combination with the Verlet-neighborlist 30 | ; scheme, Martini can be simulated with a straight cutoff. In order to 31 | ; do so, the cutoff distance is reduced 1.1 nm. 32 | ; Neighborlist length should be optimized depending on your hardware setup: 33 | ; updating ever 20 steps should be fine for classic systems, while updating 34 | ; every 30-40 steps might be better for GPU based systems. 35 | ; 36 | ; Improper neighbor list settings result in artifical pressure oscillations and 37 | ; violation of spatial isotropy. 38 | ; To avoid this, the verlet-buffer-tolerance is explicitly disabled. 39 | ; rlist should be at least 1.35 nm (with nstlist = 20 and rcoulomb/rvdw = 1.1). 40 | ; To use nstlist > 20, rlist must be further increased and tested. 41 | ; This helps to reduce the artificially large undulation amplitude of Martini membranes. 42 | ; (Position restraints might not be necessary -- to be confirmed) 43 | ; To further minimize the artifact, nstt/pcouple = n * nstlist, n is positive integer. 44 | ; 45 | ; Coulomb interactions can alternatively be treated using a reaction-field, 46 | ; giving slightly better properties. 47 | ; Please realize that electrostVatic interactions in the Martini model are 48 | ; not considered to be very accurate to begin with, especially as the 49 | ; screening in the system is set to be uniform across the system with 50 | ; a screening constant of 15. When using PME, please make sure your 51 | ; system properties are still reasonable. 52 | ; 53 | ; With the polarizable water model, the relative electrostatic screening 54 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 55 | ; apolar solvent. The polarizable water itself will perform the explicit screening 56 | ; in aqueous environment. In this case, the use of PME is more realistic. 57 | 58 | cutoff-scheme = Verlet 59 | nstlist = 20 60 | nsttcouple = 20 61 | nstpcouple = 20 62 | rlist = 1.35 63 | verlet-buffer-tolerance = -1 64 | ns_type = grid 65 | pbc = xyz 66 | 67 | coulombtype = reaction-field 68 | rcoulomb = 1.1 69 | epsilon_r = 15 ; 2.5 (with polarizable water) 70 | epsilon_rf = 0 71 | vdw_type = cutoff 72 | vdw-modifier = Potential-shift-verlet 73 | rvdw = 1.1 74 | 75 | ; MARTINI and TEMPERATURE/PRESSURE 76 | ; normal temperature and pressure coupling schemes can be used. 77 | ; It is recommended to couple individual groups in your system separately. 78 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 79 | ; thermostat using a coupling constant of the order of 1 ps. Even better 80 | ; temperature control can be achieved by reducing the temperature coupling 81 | ; constant to 0.1 ps, although with such tight coupling (approaching 82 | ; the time step) one can no longer speak of a weak-coupling scheme. 83 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 84 | ; The Berendsen thermostat is less suited since it does not give 85 | ; a well described thermodynamic ensemble. 86 | ; 87 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 88 | ; with a coupling constant in the range 4-8 ps and typical compressibility 89 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 90 | ; the Berendsen barostat probably gives better results, as the Parrinello- 91 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 92 | ; coupling should be done semiisotropic. 93 | 94 | tcoupl = v-rescale 95 | tc-grps = Solvent Rest 96 | tau_t = 1.0 1.0 97 | ref_t = 310 310 98 | 99 | gen_vel = no 100 | gen_temp = 310 101 | gen_seed = -1 102 | 103 | ; The recommended barostat is the stochastic cell rescaling barostat (c-rescale) 104 | ; due to its exponential relaxation property. Martini lipids are benchmarked 105 | ; with a coupling constant of 4 ps and compressibility 3e-4. 106 | ; C-rescale can be used for both equilibration and production simulations 107 | ; (https://doi.org/10.1063/5.0020514). 108 | ; For bilayer systems, the pressure should maintained using semiisotropic coupling. 109 | ; As of GROMACS 2023, c-rescale is not implemented for full anisotropic systems, 110 | ; but will likely be implemented (https://gitlab.com/gromacs/gromacs/-/merge_requests/3720). 111 | ; For now, full anisotropic coupling can be done using Berendsen barostat, even though 112 | ; the sampled ensemble is theoretically not NPT. The PR barostat is not recommended for 113 | ; crystal-like systems where crystal breaking (box elongation resulting in breaking) 114 | ; has been observed due to pressure oscillations. 115 | 116 | ; Pressure coupling 117 | Pcoupl = c-rescale 118 | Pcoupltype = semiisotropic 119 | tau_p = 4.0 120 | ref_p = 1.0 1.0 121 | compressibility = 3e-4 3e-4 122 | 123 | refcoord_scaling = all 124 | 125 | ; Center of mass removal 126 | comm-mode = Linear 127 | nstcomm = 100 128 | comm-grps = Rest Solvent 129 | 130 | ; MARTINI and CONSTRAINTS 131 | ; for ring systems and stiff bonds constraints are defined 132 | ; which are best handled using Lincs. 133 | 134 | constraints = none 135 | constraint_algorithm = Lincs 136 | lincs_order = 8 137 | lincs_warnangle = 90 138 | lincs_iter = 2 139 | -------------------------------------------------------------------------------- /tools/resources/martini_v2.x_new-rf-prod.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x 3 | ; Updated 15 Jul 2015 by DdJ 4 | ; 5 | ; for use with GROMACS 5 6 | ; For a thorough comparison of different mdp options in combination with the Martini force field, see: 7 | ; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted. 8 | 9 | ; TIMESTEP IN MARTINI 10 | ; Most simulations are numerically stable with dt=40 fs, 11 | ; however better energy conservation is achieved using a 12 | ; 20-30 fs timestep. 13 | ; Time steps smaller than 20 fs are not required unless specifically stated in the itp file. 14 | 15 | x_define_x 16 | integrator = md 17 | dt = 0.02 18 | nsteps = 50000000 ; 1 us 19 | 20 | nstxout = 0 21 | nstvout = 0 22 | nstfout = 0 23 | nstlog = 25000 ; 0.5 ns 24 | nstenergy = 25000 ; 0.5 ns 25 | nstxout-compressed = 50000 ; 1 ns 26 | compressed-x-precision = 100 27 | compressed-x-grps = 28 | energygrps = System 29 | 30 | ; NEIGHBOURLIST and MARTINI 31 | ; To achieve faster simulations in combination with the Verlet-neighborlist 32 | ; scheme, Martini can be simulated with a straight cutoff. In order to 33 | ; do so, the cutoff distance is reduced 1.1 nm. 34 | ; Neighborlist length should be optimized depending on your hardware setup: 35 | ; updating ever 20 steps should be fine for classic systems, while updating 36 | ; every 30-40 steps might be better for GPU based systems. 37 | ; 38 | ; Improper neighbor list settings result in artifical pressure oscillations and 39 | ; violation of spatial isotropy. 40 | ; To avoid this, the verlet-buffer-tolerance is explicitly disabled. 41 | ; rlist should be at least 1.35 nm (with nstlist = 20 and rcoulomb/rvdw = 1.1). 42 | ; To use nstlist > 20, rlist must be further increased and tested. 43 | ; This helps to reduce the artificially large undulation amplitude of Martini membranes. 44 | ; (Position restraints might not be necessary -- to be confirmed) 45 | ; To further minimize the artifact, nstt/pcouple = n * nstlist, n is positive integer. 46 | ; 47 | ; Coulomb interactions can alternatively be treated using a reaction-field, 48 | ; giving slightly better properties. 49 | ; Please realize that electrostVatic interactions in the Martini model are 50 | ; not considered to be very accurate to begin with, especially as the 51 | ; screening in the system is set to be uniform across the system with 52 | ; a screening constant of 15. When using PME, please make sure your 53 | ; system properties are still reasonable. 54 | ; 55 | ; With the polarizable water model, the relative electrostatic screening 56 | ; (epsilon_r) should have a value of 2.5, representative of a low-dielectric 57 | ; apolar solvent. The polarizable water itself will perform the explicit screening 58 | ; in aqueous environment. In this case, the use of PME is more realistic. 59 | 60 | cutoff-scheme = Verlet 61 | nstlist = 20 62 | nsttcouple = 20 63 | nstpcouple = 20 64 | rlist = 1.35 65 | verlet-buffer-tolerance = -1 66 | ns_type = grid 67 | pbc = xyz 68 | 69 | coulombtype = reaction-field 70 | rcoulomb = 1.1 71 | epsilon_r = 15 ; 2.5 (with polarizable water) 72 | epsilon_rf = 0 73 | vdw_type = cutoff 74 | vdw-modifier = Potential-shift-verlet 75 | rvdw = 1.1 76 | 77 | ; MARTINI and TEMPERATURE/PRESSURE 78 | ; normal temperature and pressure coupling schemes can be used. 79 | ; It is recommended to couple individual groups in your system separately. 80 | ; Good temperature control can be achieved with the velocity rescale (V-rescale) 81 | ; thermostat using a coupling constant of the order of 1 ps. Even better 82 | ; temperature control can be achieved by reducing the temperature coupling 83 | ; constant to 0.1 ps, although with such tight coupling (approaching 84 | ; the time step) one can no longer speak of a weak-coupling scheme. 85 | ; We therefore recommend a coupling time constant of at least 0.5 ps. 86 | ; The Berendsen thermostat is less suited since it does not give 87 | ; a well described thermodynamic ensemble. 88 | ; 89 | ; Pressure can be controlled with the Parrinello-Rahman barostat, 90 | ; with a coupling constant in the range 4-8 ps and typical compressibility 91 | ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 92 | ; the Berendsen barostat probably gives better results, as the Parrinello- 93 | ; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 94 | ; coupling should be done semiisotropic. 95 | 96 | tcoupl = v-rescale 97 | tc-grps = Solvent Rest 98 | tau_t = 1.0 1.0 99 | ref_t = 310 310 100 | 101 | gen_vel = no 102 | gen_temp = 310 103 | gen_seed = 473529 104 | 105 | ; The recommended barostat is the stochastic cell rescaling barostat (c-rescale) 106 | ; due to its exponential relaxation property. Martini lipids are benchmarked 107 | ; with a coupling constant of 4 ps and compressibility 3e-4. 108 | ; C-rescale can be used for both equilibration and production simulations 109 | ; (https://doi.org/10.1063/5.0020514). 110 | ; For bilayer systems, the pressure should maintained using semiisotropic coupling. 111 | ; As of GROMACS 2023, c-rescale is not implemented for full anisotropic systems, 112 | ; but will likely be implemented (https://gitlab.com/gromacs/gromacs/-/merge_requests/3720). 113 | ; For now, full anisotropic coupling can be done using Berendsen barostat, even though 114 | ; the sampled ensemble is theoretically not NPT. The PR barostat is not recommended for 115 | ; crystal-like systems where crystal breaking (box elongation resulting in breaking) 116 | ; has been observed due to pressure oscillations. 117 | 118 | ; Pressure coupling 119 | Pcoupl = c-rescale 120 | Pcoupltype = semiisotropic 121 | tau_p = 4.0 122 | ref_p = 1.0 1.0 123 | compressibility = 3e-4 3e-4 124 | 125 | refcoord_scaling = all 126 | 127 | ; Center of mass removal 128 | comm-mode = Linear 129 | nstcomm = 100 130 | comm-grps = Rest Solvent 131 | 132 | ; MARTINI and CONSTRAINTS 133 | ; for ring systems and stiff bonds constraints are defined 134 | ; which are best handled using Lincs. 135 | 136 | constraints = none 137 | constraint_algorithm = Lincs 138 | lincs_order = 8 139 | lincs_warnangle = 90 140 | lincs_iter = 2 141 | -------------------------------------------------------------------------------- /Martini_lipid_Benchmark/martini_benchmark_apl.csv: -------------------------------------------------------------------------------- 1 | Ref Name,Lipid Tail,APL [nm^2],Uncertainty [nm^2],T [K],NaCl [M],Ref,, 2 | DLPC,12:0/12:0,0.596,0.012,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 3 | DLPC,12:0/12:0,0.608,0.012,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 4 | DLPC,12:0/12:0,0.648,0.013,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 5 | DLPC,12:0/12:0,0.659,0.013,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 6 | ,,,,,,,, 7 | DMPC,14:0/14:0,0.599,0.012,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 8 | DMPC,14:0/14:0,0.633,0.013,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 9 | DMPC,14:0/14:0,0.657,0.013,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 10 | ,,,,,,,, 11 | DPPC,16:0/16:0,0.631,0.013,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 12 | DPPC,16:0/16:0,0.65,0.013,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 13 | ,,,,,,,, 14 | DSPC,18:0/18:0,0.638,0.013,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 15 | ,,,,,,,, 16 | MSPC,14:0/18:0,0.622,0.012,323.15,no,https://doi.org/10.3390/sym13081441,, 17 | SMPC,18:0/14:0,0.62,0.012,323.15,no,https://doi.org/10.3390/sym13081441,, 18 | PMPC,16:0/14:0,0.629,0.013,323.15,no,https://doi.org/10.3390/sym13081441,, 19 | ,,,,,,,, 20 | DRPC,14:1/14:1,0.642,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 21 | DYPC,16:1/16:1,0.658,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 22 | DOPC,18:1/18:1,0.643,0.013,293.15,no,https://doi.org/10.1039/C6SM02727J,, 23 | DOPC,18:1/18:1,0.669,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 24 | DGPC,20:1/20:1,0.666,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 25 | DEPC,22:1/22:1,0.657,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 26 | DNPC,24:1/24:1,0.627,0.01,303.15,no,https://doi.org/10.1016/j.bpj.2009.06.050,, 27 | ,,,,,,,, 28 | PSM,d18:1/16:0,0.6,0.012,318.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 29 | PSM,d18:1/16:0,0.619,0.012,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 30 | SSM,d18:1/18:0,0.625,0.013,328.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 31 | SSM,d18:1/18:0,0.649,0.013,338.15,no,https://doi.org/10.1021/acs.jpcb.0c03389,, 32 | ,,,,,,,, 33 | POPC,16:0/18:1,0.627,0.013,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 34 | POPC,16:0/18:1,0.643,0.013,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 35 | POPC,16:0/18:1,0.673,0.013,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 36 | POPC,16:0/18:1,0.681,0.014,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 37 | ,,,,,,,, 38 | SOPC,18:0/18:1,0.638,0.013,293.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 39 | SOPC,18:0/18:1,0.655,0.013,303.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 40 | SOPC,18:0/18:1,0.681,0.013,323.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 41 | SOPC,18:0/18:1,0.694,0.014,333.15,no,https://doi.org/10.1016/j.bbamem.2011.07.022,, 42 | ,,,,,,,, 43 | PDPC,16:0/22:6,0.693,0.013,293.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 44 | PDPC,16:0/22:6,0.711,0.014,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 45 | PDPC,16:0/22:6,0.729,0.015,313.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 46 | ,,,,,,,, 47 | SDPC,18:0/22:6,0.704,0.014,303.15,no,https://doi.org/10.1016/j.chemphyslip.2020.104892,, 48 | ,,,,,,,, 49 | DLPE,12:0/12:0,0.517,0.01,308.15,no,https://doi.org/10.1021/jp511159q,, 50 | DLPE,12:0/12:0,0.539,0.011,318.15,no,https://doi.org/10.1021/jp511159q,, 51 | DLPE,12:0/12:0,0.559,0.011,328.15,no,https://doi.org/10.1021/jp511159q,, 52 | ,,,,,,,, 53 | POPE,16:0/18:1,0.58,0.012,308.15,no,https://doi.org/10.1021/jp511159q,, 54 | POPE,16:0/18:1,0.592,0.012,313.15,no,https://doi.org/10.1021/jp511159q,, 55 | POPE,16:0/18:1,0.613,0.012,323.15,no,https://doi.org/10.1021/jp511159q,, 56 | ,,,,,,,, 57 | SOPE,18:0/18:1,0.568,0.011,308.15,no,https://doi.org/10.1021/jp511159q,, 58 | SOPE,18:0/18:1,0.578,0.012,313.15,no,https://doi.org/10.1021/jp511159q,, 59 | SOPE,18:0/18:1,0.601,0.012,323.15,no,https://doi.org/10.1021/jp511159q,, 60 | ,,,,,,,, 61 | DLPG,12:0/12:0,0.602,0.012,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 62 | DLPG,12:0/12:0,0.621,0.012,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 63 | DLPG,12:0/12:0,0.653,0.013,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 64 | DLPG,12:0/12:0,0.671,0.013,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 65 | ,,,,,,,, 66 | DMPG,14:0/14:0,0.625,0.013,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 67 | DMPG,14:0/14:0,0.66,0.013,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 68 | DMPG,14:0/14:0,0.675,0.014,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 69 | ,,,,,,,, 70 | DPPG,16:0/16:0,0.647,0.013,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 71 | DPPG,16:0/16:0,0.668,0.013,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 72 | ,,,,,,,, 73 | DSPG,18:0/18:0,0.668,0.013,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 74 | ,,,,,,,, 75 | POPG,16:0/18:1,0.625,0.013,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 76 | POPG,16:0/18:1,0.643,0.013,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 77 | POPG,16:0/18:1,0.684,0.014,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 78 | POPG,16:0/18:1,0.696,0.014,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 79 | ,,,,,,,, 80 | SOPG,18:0/18:1,0.629,0.013,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 81 | SOPG,18:0/18:1,0.643,0.013,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 82 | SOPG,18:0/18:1,0.676,0.014,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 83 | SOPG,18:0/18:1,0.69,0.014,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 84 | ,,,,,,,, 85 | DOPG,18:1/18:1,0.679,0.014,293.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 86 | DOPG,18:1/18:1,0.691,0.014,303.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 87 | DOPG,18:1/18:1,0.711,0.014,323.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 88 | DOPG,18:1/18:1,0.717,0.014,333.15,neutralizing,https://doi.org/10.1016/j.bbamem.2014.08.009,, 89 | ,,,,,,,, 90 | ,,,,,,,, 91 | ,,,,,,,, 92 | ,,,,,,,, 93 | ,,,,,,,, 94 | ,,,,,,,, 95 | ,,,,,,,, 96 | ,,,,,,,, 97 | ,,,,,,,, 98 | ,,,,,,,, 99 | ,,,,,,,, 100 | ,,,,,,,, 101 | ,,,,,,,, 102 | ,,,,,,,, 103 | ,,,,,,,, 104 | ,,,,,,,, 105 | ,,,,,,,, 106 | ,,,,,,,, 107 | ,,,,,,,, 108 | ,,,,,,,, 109 | ,,,,,,,, 110 | ,,,,,,,, 111 | ,,,,,,,, 112 | ,,,,,,,, 113 | ,,,,,,,, 114 | ,,,,,,,, 115 | ,,,,,,,, 116 | ,,,,,,,, 117 | ,,,,,,,, 118 | ,,,,,,,, 119 | ,,,,,,,, 120 | ,,,,,,,, 121 | ,,,,,,,, 122 | ,,,,,,,, 123 | ,,,,,,,, 124 | ,,,,,,,, 125 | ,,,,,,,, 126 | ,,,,,,,, 127 | ,,,,,,,, 128 | ,,,,,,,, 129 | ,,,,,,,, 130 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_hydrocarbons_v2.itp: -------------------------------------------------------------------------------- 1 | 2 | ;;;;; MARTINI 3.0 - Hydrocarbons 3 | ;;;;; Alkanes / Alkenes 4 | 5 | ; please cite: 6 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 7 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 8 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 9 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 10 | ; last edit Jan-2025, Kasper 11 | 12 | ;;;;; 13 | ;;;;; C16 14 | ;;;;; 15 | 16 | ;;;;; BEAD-INDEX MAPPING 17 | ;;;;; topology description 18 | ; 19 | ; C1A-C2A-C3A-C4A 1-2-3-4 20 | ; 21 | 22 | [moleculetype] 23 | C16 1 24 | 25 | [atoms] 26 | ; id type resnr residu atom cgnr charge 27 | 1 C1 1 C16 C1A 1 0 28 | 2 C1 1 C16 C2A 2 0 29 | 3 C1 1 C16 C3A 3 0 30 | 4 C1 1 C16 C4A 4 0 31 | 32 | [bonds] 33 | ; i j named potential 34 | 1 2 b_C1_C1_end 35 | 2 3 b_C1_C1_mid 36 | 3 4 b_C1_C1_end 37 | 38 | [angles] 39 | ; i j k named potential 40 | 1 2 3 a_C1_C1_C1_def 41 | 2 3 4 a_C1_C1_C1_def 42 | 43 | ;;;;; 44 | ;;;;; C20 45 | ;;;;; 46 | 47 | ;;;;; BEAD-INDEX MAPPING 48 | ;;;;; topology description 49 | ; 50 | ; C1A-C2A-C3A-C4A-C5A 1-2-3-4-5 51 | ; 52 | 53 | [moleculetype] 54 | C20 1 55 | 56 | [atoms] 57 | ; id type resnr residu atom cgnr charge 58 | 1 C1 1 C20 C1A 1 0 59 | 2 C1 1 C20 C2A 2 0 60 | 3 C1 1 C20 C3A 3 0 61 | 4 C1 1 C20 C4A 4 0 62 | 5 C1 1 C20 C5A 5 0 63 | 64 | [bonds] 65 | ; i j named potential 66 | 1 2 b_C1_C1_end 67 | 2 3 b_C1_C1_mid 68 | 3 4 b_C1_C1_mid 69 | 4 5 b_C1_C1_end 70 | 71 | [angles] 72 | ; i j k named potential 73 | 1 2 3 a_C1_C1_C1_def 74 | 2 3 4 a_C1_C1_C1_def 75 | 3 4 5 a_C1_C1_C1_def 76 | 77 | ;;;;; 78 | ;;;;; C24 79 | ;;;;; 80 | 81 | ;;;;; BEAD-INDEX MAPPING 82 | ;;;;; topology description 83 | ; 84 | ; C1A-C2A-C3A-C4A-C5A-C6A 1-2-3-4-5-6 85 | ; 86 | 87 | [moleculetype] 88 | C24 1 89 | 90 | [atoms] 91 | ; id type resnr residu atom cgnr charge 92 | 1 C1 1 C24 C1A 1 0 93 | 2 C1 1 C24 C2A 2 0 94 | 3 C1 1 C24 C3A 3 0 95 | 4 C1 1 C24 C4A 4 0 96 | 5 C1 1 C24 C5A 5 0 97 | 6 C1 1 C24 C6A 6 0 98 | 99 | [bonds] 100 | ; i j named potential 101 | 1 2 b_C1_C1_end 102 | 2 3 b_C1_C1_mid 103 | 3 4 b_C1_C1_mid 104 | 4 5 b_C1_C1_mid 105 | 5 6 b_C1_C1_end 106 | 107 | [angles] 108 | ; i j k named potential 109 | 1 2 3 a_C1_C1_C1_def 110 | 2 3 4 a_C1_C1_C1_def 111 | 3 4 5 a_C1_C1_C1_def 112 | 4 5 6 a_C1_C1_C1_def 113 | 114 | ;;;;; 115 | ;;;;; IC1 116 | ;;;;; 117 | 118 | ;;;;; BEAD-INDEX MAPPING 119 | ;;;;; topology description 120 | ; 121 | ; C1A-C2A-D3A-C4A-C5A 1-2-3-4-5 122 | ; 123 | 124 | [moleculetype] 125 | IC1 1 126 | 127 | [atoms] 128 | ; id type resnr residu atom cgnr charge 129 | 1 C1 1 IC1 C1A 1 0 130 | 2 C1 1 IC1 C2A 2 0 131 | 3 C4h 1 IC1 D3A 3 0 132 | 4 C1 1 IC1 C4A 4 0 133 | 5 C1 1 IC1 C5A 5 0 134 | 135 | [bonds] 136 | ; i j named potential 137 | 1 2 b_C1_C1_end 138 | 2 3 b_C1_C4_mid 139 | 3 4 b_C1_C4_mid 140 | 4 5 b_C1_C1_end 141 | 142 | [angles] 143 | ; i j k named potential 144 | 1 2 3 a_C1_C1_C4_def 145 | 2 3 4 a_C1_C4_C1_def 146 | 3 4 5 a_C1_C1_C4_def 147 | 148 | ;;;;; 149 | ;;;;; IC2 150 | ;;;;; 151 | 152 | ;;;;; BEAD-INDEX MAPPING 153 | ;;;;; topology description 154 | ; 155 | ; C1A-C2A-D3A-D4A-C5A 1-2-3-4-5 156 | ; 157 | 158 | [moleculetype] 159 | IC2 1 160 | 161 | [atoms] 162 | ; id type resnr residu atom cgnr charge 163 | 1 C1 1 IC2 C1A 1 0 164 | 2 C1 1 IC2 C2A 2 0 165 | 3 C4h 1 IC2 D3A 3 0 166 | 4 C4h 1 IC2 D4A 4 0 167 | 5 C1 1 IC2 C5A 5 0 168 | 169 | [bonds] 170 | ; i j named potential 171 | 1 2 b_C1_C1_end 172 | 2 3 b_C1_C4_mid 173 | 3 4 b_C4_C4_mid 174 | 4 5 b_C1_C4_mid 175 | 176 | [angles] 177 | ; i j k named potential 178 | 1 2 3 a_C1_C1_C4_def 179 | 2 3 4 a_C1_C4_C4_def 180 | 3 4 5 a_C1_C4_C4_def 181 | 182 | ;;;;; 183 | ;;;;; IC3 184 | ;;;;; 185 | 186 | ;;;;; BEAD-INDEX MAPPING 187 | ;;;;; topology description 188 | ; 189 | ; C1A-C2A-D3A-D4A-D5A 1-2-3-4-5 190 | ; 191 | 192 | [moleculetype] 193 | IC3 1 194 | 195 | [atoms] 196 | ; id type resnr residu atom cgnr charge 197 | 1 C1 1 IC3 C1A 1 0 198 | 2 C1 1 IC3 C2A 2 0 199 | 3 C4h 1 IC3 D3A 3 0 200 | 4 C4h 1 IC3 D4A 4 0 201 | 5 C4h 1 IC3 D5A 5 0 202 | 203 | [bonds] 204 | ; i j named potential 205 | 1 2 b_C1_C1_end 206 | 2 3 b_C1_C4_mid 207 | 3 4 b_C4_C4_mid 208 | 4 5 b_C4_C4_mid 209 | 210 | [angles] 211 | ; i j k named potential 212 | 1 2 3 a_C1_C1_C4_def 213 | 2 3 4 a_C1_C4_C4_def 214 | 3 4 5 a_C4_C4_C4_def 215 | 216 | ;;;;; 217 | ;;;;; IC4 218 | ;;;;; 219 | 220 | ;;;;; BEAD-INDEX MAPPING 221 | ;;;;; topology description 222 | ; 223 | ; C1A-D2A-D3A-D4A-D5A 1-2-3-4-5 224 | ; 225 | 226 | [moleculetype] 227 | IC4 1 228 | 229 | [atoms] 230 | ; id type resnr residu atom cgnr charge 231 | 1 C1 1 IC4 C1A 1 0 232 | 2 C4h 1 IC4 D2A 2 0 233 | 3 C5h 1 IC4 D3A 3 0 234 | 4 C4h 1 IC4 D4A 4 0 235 | 5 C4h 1 IC4 D5A 5 0 236 | 237 | [bonds] 238 | ; i j named potential 239 | 1 2 b_C1_C4_mid 240 | 2 3 b_C4_C4_mid 241 | 3 4 b_C4_C4_mid 242 | 4 5 b_C4_C4_mid 243 | 244 | [angles] 245 | ; i j k named potential 246 | 1 2 3 a_C1_C4_C4_def 247 | 2 3 4 a_C4_C4_C4_def 248 | 3 4 5 a_C4_C4_C4_def 249 | 250 | ;;;;; 251 | ;;;;; IC5 252 | ;;;;; 253 | 254 | ;;;;; BEAD-INDEX MAPPING 255 | ;;;;; topology description 256 | ; 257 | ; C1A-D2A-D3A-D4A-D5A 1-2-3-4-5 258 | ; 259 | 260 | [moleculetype] 261 | IC5 1 262 | 263 | [atoms] 264 | ; id type resnr residu atom cgnr charge 265 | 1 C1 1 IC5 C1A 1 0 266 | 2 C5h 1 IC5 D2A 2 0 267 | 3 C5h 1 IC5 D3A 3 0 268 | 4 C4h 1 IC5 D4A 4 0 269 | 5 C4h 1 IC5 D5A 5 0 270 | 271 | [bonds] 272 | ; i j named potential 273 | 1 2 b_C1_C4_mid 274 | 2 3 b_C4_C4_mid 275 | 3 4 b_C4_C4_mid 276 | 4 5 b_C4_C4_mid 277 | 278 | [angles] 279 | ; i j k named potential 280 | 1 2 3 a_C1_C4_C4_def 281 | 2 3 4 a_C4_C4_C4_def 282 | 3 4 5 a_C4_C4_C4_def 283 | 284 | ;;;;; 285 | ;;;;; IC6 286 | ;;;;; 287 | 288 | ;;;;; BEAD-INDEX MAPPING 289 | ;;;;; topology description 290 | ; 291 | ; C1A-D2A-C3A-C4A-C5A 1-2-3-4-5 292 | ; 293 | 294 | [moleculetype] 295 | IC6 1 296 | 297 | [atoms] 298 | ; id type resnr residu atom cgnr charge 299 | 1 C1 1 IC6 C1A 1 0 300 | 2 C4h 1 IC6 D2A 2 0 301 | 3 C1 1 IC6 C3A 3 0 302 | 4 C1 1 IC6 C4A 4 0 303 | 5 C1 1 IC6 C5A 5 0 304 | 305 | [bonds] 306 | ; i j named potential 307 | 1 2 b_C1_C4_mid 308 | 2 3 b_C1_C4_mid 309 | 3 4 b_C1_C1_mid 310 | 4 5 b_C1_C1_end 311 | 312 | [angles] 313 | ; i j k named potential 314 | 1 2 3 a_C1_C4_C1_def 315 | 2 3 4 a_C1_C1_C4_def 316 | 3 4 5 a_C1_C1_C1_def 317 | 318 | ;;;;; 319 | ;;;;; IC7 320 | ;;;;; 321 | 322 | ;;;;; BEAD-INDEX MAPPING 323 | ;;;;; topology description 324 | ; 325 | ; C1A-D2A-C3A-D4A-D5A 1-2-3-4-5 326 | ; 327 | 328 | [moleculetype] 329 | IC7 1 330 | 331 | [atoms] 332 | ; id type resnr residu atom cgnr charge 333 | 1 C1 1 IC7 C1A 1 0 334 | 2 C4h 1 IC7 D2A 2 0 335 | 3 C1 1 IC7 C3A 3 0 336 | 4 C4h 1 IC7 D4A 4 0 337 | 5 C4h 1 IC7 D5A 5 0 338 | 339 | [bonds] 340 | ; i j named potential 341 | 1 2 b_C1_C4_mid 342 | 2 3 b_C1_C4_mid 343 | 3 4 b_C1_C4_mid 344 | 4 5 b_C4_C4_mid 345 | 346 | [angles] 347 | ; i j k named potential 348 | 1 2 3 a_C1_C4_C1_def 349 | 2 3 4 a_C4_C1_C4_def 350 | 3 4 5 a_C1_C4_C4_def 351 | 352 | ;;;;; 353 | ;;;;; IC8 354 | ;;;;; 355 | 356 | ;;;;; BEAD-INDEX MAPPING 357 | ;;;;; topology description 358 | ; 359 | ; C1A-D2A-C3A-D4A-C5A 1-2-3-4-5 360 | ; 361 | 362 | [moleculetype] 363 | IC8 1 364 | 365 | [atoms] 366 | ; id type resnr residu atom cgnr charge 367 | 1 C1 1 IC8 C1A 1 0 368 | 2 C4h 1 IC8 D2A 2 0 369 | 3 C1 1 IC8 C3A 3 0 370 | 4 C4h 1 IC8 D4A 4 0 371 | 5 C1 1 IC8 C5A 5 0 372 | 373 | [bonds] 374 | ; i j named potential 375 | 1 2 b_C1_C4_mid 376 | 2 3 b_C1_C4_mid 377 | 3 4 b_C1_C4_mid 378 | 4 5 b_C1_C4_mid 379 | 380 | [angles] 381 | ; i j k named potential 382 | 1 2 3 a_C1_C4_C1_def 383 | 2 3 4 a_C4_C1_C4_def 384 | 3 4 5 a_C1_C4_C1_def 385 | 386 | ;;;;; 387 | ;;;;; IC9 388 | ;;;;; 389 | 390 | ;;;;; BEAD-INDEX MAPPING 391 | ;;;;; topology description 392 | ; 393 | ; C1A-D2A-C3A-C4A-D5A 1-2-3-4-5 394 | ; 395 | 396 | [moleculetype] 397 | IC9 1 398 | 399 | [atoms] 400 | ; id type resnr residu atom cgnr charge 401 | 1 C1 1 IC9 C1A 1 0 402 | 2 C4h 1 IC9 D2A 2 0 403 | 3 C1 1 IC9 C3A 3 0 404 | 4 C1 1 IC9 C4A 4 0 405 | 5 C4h 1 IC9 D5A 5 0 406 | 407 | [bonds] 408 | ; i j named potential 409 | 1 2 b_C1_C4_mid 410 | 2 3 b_C1_C4_mid 411 | 3 4 b_C1_C1_mid 412 | 4 5 b_C1_C4_mid 413 | 414 | [angles] 415 | ; i j k named potential 416 | 1 2 3 a_C1_C4_C1_def 417 | 2 3 4 a_C4_C1_C1_def 418 | 3 4 5 a_C1_C1_C4_def 419 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_ions_v1.itp: -------------------------------------------------------------------------------- 1 | ;;;;; Martini 3 - Database of ions and charged molecules. 2 | ;;;;; 3 | ;;;;; File updated on 2021-03-29 4 | ;;;;; 5 | ;;;;; Version: 3.0.0_v1 6 | ;;;;; 7 | ;;;;; This collection contains the models included as part of the Martini 3 publication: 8 | ;;;;; PCT Souza, et al., Nat. Methods, 2021. DOI: 10.1038/s41592-021-01098-3 9 | 10 | ;;;;;;;;; SIMPLE IONS (1 bead) 11 | 12 | ;;;;;; Sodium ion 13 | 14 | [moleculetype] 15 | ; molname nrexcl 16 | NA 1 17 | 18 | [atoms] 19 | ;id type resnr residu atom cgnr charge 20 | 1 TQ5 1 ION NA 1 1.0 21 | 22 | ;;;;;; Chloride ion 23 | 24 | [moleculetype] 25 | ; molname nrexcl 26 | CL 1 27 | 28 | [atoms] 29 | ;id type resnr residu atom cgnr charge 30 | 1 TQ5 1 ION CL 1 -1.0 35.453 31 | 32 | ;;;;;; Bromide ion 33 | 34 | [moleculetype] 35 | ; molname nrexcl 36 | BR 1 37 | 38 | [atoms] 39 | ;id type resnr residu atom cgnr charge mass 40 | 1 SQ4 1 ION BR 1 -1.0 79.90 41 | 42 | ;;;;;; Iodine ion 43 | 44 | [moleculetype] 45 | ; molname nrexcl 46 | IOD 1 47 | 48 | [atoms] 49 | ;id type resnr residu atom cgnr charge mass 50 | 1 SQ2 1 ION ID 1 -1.0 79.90 51 | 52 | 53 | ;;;;;; Tetramethyl amonium ion 54 | 55 | [moleculetype] 56 | ; molname nrexcl 57 | TMA 1 58 | 59 | [atoms] 60 | ;id type resnr residu atom cgnr charge 61 | 1 Q2 1 ION TMA 1 1.0 74.14 62 | 63 | ;;;;;; Acetate ion 64 | 65 | [moleculetype] 66 | ; molname nrexcl 67 | ACE 1 68 | 69 | [atoms] 70 | ;id type resnr residu atom cgnr charge 71 | 1 SQ5n 1 ION CL 1 -1.0 59.044 72 | 73 | ;;;;;; Calcium ion 74 | 75 | [moleculetype] 76 | ; molname nrexcl 77 | CA 1 78 | 79 | [atoms] 80 | ;id type resnr residu atom cgnr charge 81 | 1 SD 1 ION CA 1 2.0 40.078 ; TD may be a good option as well. 82 | 83 | ;;;;;; Tetrafluoroborate ion 84 | 85 | [moleculetype] 86 | ; molname nrexcl 87 | BF4 1 88 | 89 | [atoms] 90 | ;id type resnr residu atom cgnr charge mass 91 | 1 Q2 1 ION BF4 1 -1.0 86.80 92 | 93 | ;;;;;; Hexafluorophosphate ion 94 | 95 | [moleculetype] 96 | ; molname nrexcl 97 | PF6 1 98 | 99 | [atoms] 100 | ;id type resnr residu atom cgnr charge mass 101 | 1 Q1 1 ION PF6 1 -1.0 144.96 102 | 103 | ;;;;;; Thiocyanate ion 104 | 105 | [moleculetype] 106 | ; molname nrexcl 107 | SCN 1 108 | 109 | [atoms] 110 | ;id type resnr residu atom cgnr charge mass 111 | 1 SQ1 1 ION SCN 1 -1.0 58.08 112 | 113 | ;;;;;;;; Perchlorate anion 114 | 115 | [moleculetype] 116 | ; molname nrexcl 117 | CLO4 1 118 | 119 | [atoms] 120 | ;id type resnr residu atom cgnr charge mass 121 | 1 Q2 1 ION CLO 1 -1.0 99.45 122 | 123 | ;;;;;;;; Nitrate anion 124 | 125 | [moleculetype] 126 | ; molname nrexcl 127 | NO3 1 128 | 129 | [atoms] 130 | ;id type resnr residu atom cgnr charge mass 131 | 1 SQ3n 1 ION NO3 1 -1.0 62.005 132 | 133 | ;;;;;;;;; BIG IONS USED IN IONIC LIQUIDS 134 | 135 | ;;;;;; 1-Methyl-3-methylimidazolium ion 136 | 137 | [moleculetype] 138 | ; Name nrexcl 139 | MIM 1 140 | 141 | [ atoms ] 142 | ;id type resnr residu atom cgnr charge mass 143 | 1 TN2q 1 MIM SI1 1 0.500 32.38 144 | 2 TN2q 1 MIM SI2 2 0.500 32.38 145 | 3 TC6 1 MIM SI3 3 0.000 32.38 146 | 147 | [constraints] 148 | ; i j funct length 149 | 2 3 1 0.318 150 | 2 1 1 0.318 151 | 3 1 1 0.318 152 | 153 | ;;;;;; 1-Ethyl-3-methylimidazolium ion 154 | 155 | [moleculetype] 156 | ; Name nrexcl 157 | EIM 1 158 | 159 | [ atoms ] 160 | ;id type resnr residu atom cgnr charge 161 | 1 SN2q 1 EIM SI1 1 0.500 46.40 162 | 2 TN2q 1 EIM SI2 2 0.500 32.38 163 | 3 TC6 1 EIM SI3 3 0.000 32.38 164 | 165 | 166 | [constraints] 167 | ; i j funct length 168 | 2 3 1 0.355 169 | 2 1 1 0.318 170 | 3 1 1 0.318 171 | 172 | ;;;;;; 1-Butyl-3-methylimidazolium ion 173 | 174 | [moleculetype ] 175 | ; Name nrexcl 176 | BIM 1 177 | 178 | [ atoms ] 179 | ;id type resnr residu atom cgnr charge mass 180 | 1 TN2q 1 BIM SI1 1 0.500 31.37 181 | 2 TN2q 1 BIM SI2 2 0.500 32.38 182 | 3 TC6 1 BIM SI3 3 0.000 32.38 183 | 4 SC3 1 BIM SI4 4 0.000 43.09 184 | 185 | [bonds] 186 | ; i j funct length force.c. 187 | 1 4 1 0.340 7500 188 | 189 | [constraints] 190 | ; i j funct length 191 | 2 3 1 0.318 192 | 2 1 1 0.318 193 | 3 1 1 0.318 194 | 195 | [angles] 196 | ; i j k funct angle force.c. 197 | 3 1 4 2 120.000 50.0 198 | 2 1 4 2 120.000 50.0 199 | 200 | [dihedrals] 201 | ; i j k l funct angle force.c. 202 | 4 2 3 1 2 0.0 200.0 ; 203 | 204 | ;;;;;; 1-Octyl-3-methylimidazolium ion 205 | 206 | [moleculetype ] 207 | ; Name nrexcl 208 | OIM 1 209 | 210 | [ atoms ] 211 | ;id type resnr residu atom cgnr charge mass 212 | 1 TN2q 1 OIM SI1 1 0.500 31.37 213 | 2 TN2q 1 OIM SI2 2 0.500 32.38 214 | 3 TC6 1 OIM SI3 3 0.000 32.38 215 | 4 SC3 1 OIM SI4 4 0.000 43.09 216 | 5 C1 1 OIM SI5 4 0.000 57.11 217 | 218 | [bonds] 219 | ; i j funct length force.c. 220 | 1 4 1 0.335 7500 221 | 4 5 1 0.410 2500 222 | 223 | [constraints] 224 | ; i j funct length 225 | 2 3 1 0.318 226 | 2 1 1 0.318 227 | 3 1 1 0.318 228 | 229 | [angles] 230 | ; i j k funct angle force.c. 231 | 3 1 4 2 120.000 50.0 232 | 2 1 4 2 120.000 50.0 233 | 1 4 5 2 180.000 25.0 234 | 235 | [dihedrals] 236 | ; i j k l funct angle force.c. 237 | 4 2 3 1 2 0.0 200.0 ; 238 | 239 | ;;;;;; 1-Dodecyl -3-methylimidazolium ion 240 | 241 | [moleculetype ] 242 | ; Name nrexcl 243 | DIM 1 244 | 245 | [ atoms ] 246 | ;id type resnr residu atom cgnr charge mass 247 | 1 TN2q 1 DIM SI1 1 0.500 31.37 248 | 2 TN2q 1 DIM SI2 2 0.500 32.38 249 | 3 TC6 1 DIM SI3 3 0.000 32.38 250 | 4 SC3 1 DIM SI4 4 0.000 43.09 251 | 5 C1 1 DIM SI5 5 0.000 56.11 252 | 6 C1 1 DIM SI6 6 0.000 57.11 253 | 254 | [bonds] 255 | ; i j funct length force.c. 256 | 1 4 1 0.335 7500 257 | 4 5 1 0.405 4000 258 | 5 6 1 0.475 3800 259 | 260 | 261 | [constraints] 262 | ; i j funct length 263 | 2 3 1 0.318 264 | 2 1 1 0.318 265 | 3 1 1 0.318 266 | 267 | [angles] 268 | ; i j k funct angle force.c. 269 | 3 1 4 2 120.000 50.0 270 | 2 1 4 2 120.000 50.0 271 | 4 5 6 2 180.000 25.0 272 | 273 | [dihedrals] 274 | ; i j k l funct angle force.c. 275 | 4 2 3 1 2 0.0 200.0 ; 276 | 277 | ;;;;;; trihexyl(tetradecyl)phoshonium 278 | 279 | 280 | [ moleculetype ] 281 | ; Name nrexcl 282 | PHO 1 ; 764.002 283 | 284 | [ atoms ] 285 | ;id type resnr residu atom cgnr charge mass 286 | 1 Q1 1 PHO P1 1 1.000 87.08 287 | 2 TC3 1 PHO C2 2 0.000 28.05 288 | 3 SC2 1 PHO C3 3 0.000 43.09 289 | 4 TC3 1 PHO C4 4 0.000 28.05 290 | 5 SC2 1 PHO C5 5 0.000 43.09 291 | 6 TC3 1 PHO C6 6 0.000 28.05 292 | 7 SC2 1 PHO C7 7 0.000 43.09 293 | 8 TC3 1 PHO C8 8 0.000 28.05 294 | 9 SC2 1 PHO C9 9 0.000 42.08 295 | 10 C1 1 PHO C10 10 0.000 56.11 296 | 11 C1 1 PHO C11 11 0.000 57.11 297 | 298 | [bonds] 299 | ; i j funct length force.c. 300 | 1 2 1 0.360 5000 301 | 2 3 1 0.320 5000 302 | 1 4 1 0.360 5000 303 | 4 5 1 0.320 5000 304 | 1 6 1 0.360 5000 305 | 6 7 1 0.320 5000 306 | 1 8 1 0.360 5000 307 | 8 9 1 0.320 5000 308 | 9 10 1 0.440 3800 309 | 10 11 1 0.470 3800 310 | 311 | [angles] 312 | ; i j k funct angle force.c. 313 | 2 1 4 2 109.500 200.0 314 | 2 1 6 2 109.500 200.0 315 | 2 1 8 2 109.500 200.0 316 | 4 1 6 2 109.500 200.0 317 | 4 1 8 2 109.500 200.0 318 | 6 1 8 2 109.500 50.0 319 | 1 2 3 2 180.000 25.0 320 | 1 4 5 2 180.000 25.0 321 | 1 6 7 2 180.000 25.0 322 | 1 8 9 2 180.000 25.0 323 | 8 9 10 2 180.000 25.0 324 | 9 10 11 2 180.000 25.0 325 | 326 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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While redistributing 166 | the Work or Derivative Works thereof, You may choose to offer, 167 | and charge a fee for, acceptance of support, warranty, indemnity, 168 | or other liability obligations and/or rights consistent with this 169 | License. However, in accepting such obligations, You may act only 170 | on Your own behalf and on Your sole responsibility, not on behalf 171 | of any other Contributor, and only if You agree to indemnify, 172 | defend, and hold each Contributor harmless for any liability 173 | incurred by, or claims asserted against, such Contributor by reason 174 | of your accepting any such warranty or additional liability. 175 | 176 | END OF TERMS AND CONDITIONS 177 | 178 | -------------------------------------------------------------------------------- /tools/analysis_pipeline/area_lipid_g5.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | # ---------- Imports -------------------------- 4 | 5 | import sys,os,math,random,subprocess,numpy 6 | import re 7 | import shlex 8 | 9 | # ---------- Description ---------------------- 10 | 11 | desc = """ 12 | Compute the projected area per lipid (A_0) and area compressibility modulus (K_A). 13 | Using "Box-X" and "Box-Y" extracted from an energy file given in the arguments and 14 | dividing this area with the given number of lipids in each monolayer. 15 | 16 | See for example {Marrink, Vries, Mark, J. Phys. Chem. 2004, 108:750-760} and {Feller 17 | SE and Pastor RW, J. Chem. Phys. 1999, 111:1281-1287}. 18 | Small system will overestimate the K(A) 19 | K(A) = kT / (N<(A - A0)2>) 20 | 21 | USAGE: %s <.edr file> <#lipids in a monolayer> > ener-area-out.xvg 22 | 23 | WARNING: will override/output data to ener-area.xvg, ener-area-A0-block.xvg and ener-area-KA-block.xvg 24 | 25 | @author Helgi I. Ingolfsson 2012.08 26 | 27 | EDITS: Harvey Mudd Clinic team, 2018. Slight formatting change to make main code a function 28 | instead of a script taking in command line arguments. This was done in order to call the 29 | code from inside a larger analysis file. Also commented out several print statements. The 30 | return value is area compressibility, but can be changed 31 | EDITS: 2022.09.09 - Removed dependance on Mara_Python3.IO import XVGIO by adding parse_xvg function from analysis pipeline 32 | 33 | """ % (sys.argv[0]) 34 | 35 | 36 | # ---------- Functions/procedures ------------- 37 | 38 | # Call system or print (if in test mode) 39 | test = False #True #False # set to True for print only and False for exicuting commands 40 | def sys_call(command): 41 | if test: 42 | print(command) 43 | return 0 44 | else: 45 | p = subprocess.Popen(command, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE, stdin=subprocess.PIPE) 46 | return p.wait() 47 | 48 | # function from analysis pipeline 49 | # Functions for handling xvg files 50 | def parse_xvg(fname, sel_columns='all'): 51 | """Parses XVG file legends and data""" 52 | 53 | _ignored = set(('legend', 'view')) 54 | _re_series = re.compile('s[0-9]+$') 55 | _re_xyaxis = re.compile('[xy]axis$') 56 | 57 | metadata = {} 58 | num_data = [] 59 | 60 | metadata['labels'] = {} 61 | metadata['labels']['series'] = [] 62 | 63 | ff_path = os.path.abspath(fname) 64 | if not os.path.isfile(ff_path): 65 | raise IOError('File not readable: {0}'.format(ff_path)) 66 | 67 | with open(ff_path, 'r') as fhandle: 68 | for line in fhandle: 69 | line = line.strip() 70 | if line.startswith('@'): 71 | tokens = shlex.split(line[1:]) 72 | if tokens[0] in _ignored: 73 | continue 74 | elif tokens[0] == 'TYPE': 75 | if tokens[1] != 'xy': 76 | raise ValueError('Chart type unsupported: \'{0}\'. Must be \'xy\''.format(tokens[1])) 77 | elif _re_series.match(tokens[0]): 78 | metadata['labels']['series'].append(tokens[-1]) 79 | elif _re_xyaxis.match(tokens[0]): 80 | metadata['labels'][tokens[0]] = tokens[-1] 81 | elif len(tokens) == 2: 82 | metadata[tokens[0]] = tokens[1] 83 | else: 84 | print('Unsupported entry: {0} - ignoring'.format(tokens[0]), file=sys.stderr) 85 | elif line[0].isdigit(): 86 | num_data.append(map(float, line.split())) 87 | 88 | num_data = list(zip(*num_data)) 89 | 90 | if not metadata['labels']['series']: 91 | for series in range(len(num_data) - 1): 92 | metadata['labels']['series'].append('') 93 | 94 | # Column selection if asked 95 | if sel_columns != 'all': 96 | sel_columns = map(int, sel_columns) 97 | x_axis = num_data[0] 98 | num_data = [x_axis] + [num_data[col] for col in sel_columns] 99 | metadata['labels']['series'] = [metadata['labels']['series'][col - 1] for col in sel_columns] 100 | 101 | return metadata, num_data 102 | 103 | # ---------- Parse input/display help --------- 104 | def calculate_area_compressibility(ene_file, runDir, begin_time, end_time, lipids_per_mon, temperature): 105 | # Read input 106 | #args = sys.argv[1:] 107 | 108 | #if '-h' in args or '--help' in args or len(args) != 5: 109 | # print(desc) 110 | # sys.exit() 111 | 112 | procString = "area-lipid.py from file " + ene_file + " starting " + str(begin_time) + " to " + str(end_time) + " lipid count " + str(lipids_per_mon) + " temperature " + str(temperature) 113 | # print procString 114 | 115 | # ensure that inputs are ints 116 | #begin_time = int(begin_time) 117 | #end_time = int(end_time) 118 | #lipids_per_mon = float(lipids_per_mon) 119 | #temperature = float(temperature) 120 | 121 | ene_out_file = runDir + '/ener-area.xvg' 122 | block_A0_out_file = runDir + '/ener-area-A0-block.xvg' 123 | block_KA_out_file = runDir + '/ener-area-KA-block.xvg' 124 | 125 | scaled_k = 0.013806488 # Boltzmann constant (1.3806488 x 10^23 J/K, but here scaled so final K(A) values is in mN/m) 126 | 127 | # ---------- Start script --------------------- 128 | 129 | # print "Projected area per lipid (A_0) mean, sd and se (se is from block averaging see " + block_A0_out_file + ")" 130 | # print "and area compressibility modulus (K_A) men, sd and se (sd and se are from block averaging see " + block_KA_out_file + ")" 131 | 132 | sys_call('echo -e "Box-X\nBox-Y\n 0" | gmx energy -f ' + ene_file + ' -b ' + str(begin_time) + ' -e ' + str(end_time) + ' -o ' + ene_out_file) 133 | 134 | # read xvg files 135 | metadata, num_data = parse_xvg(ene_out_file) 136 | # As we only saved x2 values box-X is num_data[1][x] and box-Y is num_data[2][x] 137 | #print(f"Read from enegery file - metadata {metadata}") 138 | #print(f"Read from enegery file - len {len(num_data)} len1 {len(num_data[0])} len2 {len(num_data[1])}") 139 | 140 | line_count = len(num_data[1]) 141 | area = numpy.zeros(line_count) 142 | area_lipid = numpy.zeros(line_count) 143 | sum = 0 144 | 145 | # Calculate area and area/per lipid - for each timepoint 146 | for ti in range(line_count): 147 | #area[ti] = set[0][ti] * set[1][ti] 148 | area[ti] = num_data[1][ti] * num_data[2][ti] # num_data[0] is the time step 149 | area_lipid[ti] = area[ti] / lipids_per_mon 150 | # End for 151 | 152 | # Get ave +/- sd for area per lipid 153 | val_A0 = numpy.average(area_lipid) 154 | val_A0_sd_r = numpy.std(area_lipid) 155 | 156 | # Use block averaging to get the SD and SE of the average area per lipid 157 | # Use minimum x5 blocks, report SD SE as max value in the last 20% in block curve 158 | outFile = open(block_A0_out_file,"w") 159 | print('#' + procString, file=outFile) 160 | print('# block averaging for A_0', file=outFile) 161 | block_max = int(line_count/5) 162 | block_range = range(1, block_max, 5) 163 | block_in_top_20 = block_max * 0.8 164 | val_A0_sd = -1 165 | val_A0_se = -1 166 | for block_size in block_range: 167 | blocks = range(block_size, line_count+1, block_size) 168 | numBlocks = int(line_count / block_size) 169 | blocked_A0 = [] 170 | index = 0 171 | last_block = 0 172 | for ti in blocks: 173 | blocked_A0.append(numpy.average(area_lipid[(ti-block_size):ti])) 174 | # End for 175 | 176 | currentSTD = numpy.std(blocked_A0) 177 | currentSE = currentSTD / math.sqrt(numBlocks) 178 | print("%7i %10.8f %10.8f %10.8f" % (block_size, numpy.average(blocked_A0), currentSTD, currentSE), file=outFile) 179 | 180 | if (block_size >= block_in_top_20): 181 | if val_A0_sd < currentSTD: 182 | val_A0_sd = currentSTD 183 | if val_A0_se < currentSE: 184 | val_A0_se = currentSE 185 | 186 | # End for 187 | outFile.close() 188 | # Warning here the SD is the SD of the preaveraged, the SD we report is val_A0_sd_r (same as sd with block size of 1) 189 | # print "Average +/- sd projected area per lipid: %.5f sd %.5f se %.5f (nm^2)" % (val_A0, val_A0_sd_r, val_A0_se) 190 | 191 | 192 | # Calculate area compressibility modulus K(A) = kTA0 / N<(A - A0)^2> 193 | val_ave_area_var = 0 194 | area_lipid_squear_diff = numpy.zeros(line_count) 195 | # For each timepoint 196 | for ti in range(line_count): 197 | area_lipid_squear_diff[ti] = (area_lipid[ti] - val_A0)**2 198 | val_ave_area_var += area_lipid_squear_diff[ti] 199 | # End for 200 | val_ave_area_var = val_ave_area_var / line_count 201 | val_scaling = (scaled_k * temperature * val_A0) / lipids_per_mon # kT A0 / N 202 | val_KA = val_scaling * (1 / val_ave_area_var) 203 | 204 | # Calculate SD for area compressibility modulus K(A) - need to do block averaging 205 | # Use minimum x5 blocks, report SD SE as max value in the last 20% in block curve 206 | outFile = open(block_KA_out_file,"w") 207 | print('#' + procString, file=outFile) 208 | print('# block averaging for K_A', file=outFile) 209 | block_max = int(line_count/5) 210 | block_range = range(1, block_max, 5) 211 | block_in_top_20 = block_max * 0.8 212 | val_KA_sd = -1 213 | val_KA_se = -1 214 | for block_size in block_range: 215 | blocks = range(block_size, line_count, block_size) 216 | numBlocks = int(line_count / block_size) 217 | blocked_A0 = [] 218 | index = 0 219 | for ti in blocks: 220 | #print ti 221 | current_block = [] 222 | while (index < ti): 223 | #print "inner %i %i " % (ti, index) 224 | #current_block.append((area_lipid[index] - val_A0)**2) 225 | current_block.append(area_lipid_squear_diff[index]) 226 | index += 1 227 | 228 | blocked_A0.append(val_scaling * (1 / numpy.average(current_block))) 229 | # End for 230 | 231 | currentSTD = numpy.std(blocked_A0) 232 | currentSE = currentSTD / math.sqrt(numBlocks) 233 | print("%7i %10.8f %10.8f %10.8f" % (block_size, numpy.average(blocked_A0), currentSTD, currentSE), file=outFile) 234 | 235 | if (block_size >= block_in_top_20): 236 | if val_KA_sd < currentSTD: 237 | val_KA_sd = currentSTD 238 | if val_KA_se < currentSE: 239 | val_KA_se = currentSE 240 | # End for 241 | outFile.close() 242 | 243 | # print "Calculate compressibility moduleus: ave %.5f sd %.5f se %.5f (mN/m)" % (val_KA, val_KA_sd, val_KA_se) 244 | #return (val_KA, val_KA_se) 245 | return (val_A0, val_A0_sd_r, val_A0_se, val_KA, val_KA_sd, val_KA_se) 246 | 247 | # sys.exit(0) 248 | 249 | # ---------- End script ----------------------- 250 | 251 | 252 | 253 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_ffbonded_v2.itp: -------------------------------------------------------------------------------- 1 | ; GENERALIZED NAMED BONDED TYPES FOR THE MARTINI 3 MODEL 2 | ; Here we present a list of basic parameters, which can be used as defaults 3 | ; or for starting point for further optimization 4 | ; 5 | ; All definitions are named _ < 2-4 bead names > _ extra specification 6 | ; e.g. a_GL_C1_C4_glyc (angle between GL-C1-C4 beads for glyc parameters) 7 | ; 8 | ; If you use these parameters, please cite: 9 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 10 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 11 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 12 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 13 | ; Last edit Jan-2025, Kasper B. Pedersen 14 | ; 15 | ; Changes from beta_v3 (only renaming and comments): 16 | ; Removed CBT dihedrals 17 | ; replaced "_cbt" with "" 18 | ; replaced "_lipid" with "_def" 19 | ; add params replaced "_glyc" with "_ether" for etherlipids 20 | ; add params replaced "_glyc" with "_plasm" for plasmalogens 21 | 22 | ;;;;; 23 | ;;;;; ALKANES / ALKENES 24 | ;;;;; 25 | 26 | [ bondtypes ] 27 | ; name type length k 28 | ; bonds between regular carbon beads containing 4 atoms each: 29 | #define b_C1_C1_mid 1 0.490 2800.0 ; default R-R distance in the middle of an alkane chain 30 | #define b_C1_C4_mid 1 0.475 2800.0 ; containing a double bond in one bead 31 | #define b_C4_C1_mid 1 0.475 2800.0 ; symmetric, same as b_C1_C4_mid 32 | #define b_C4_C4_mid 1 0.460 2800.0 ; containing a double bond in both beads 33 | #define b_C1_C1_end 1 0.500 2800.0 ; at the end of the chain, internal conformations in AA reference results in a longer bond on average 34 | #define b_C4_C1_end 1 0.485 2800.0 35 | #define b_C1_C4_end 1 0.485 2800.0 36 | #define b_C4_C4_end 1 0.470 2800.0 37 | ; bonds between a regular 5 carbon bead and a regular 4 carbon bead: 38 | #define b_C1_C1_mid_5long 1 0.520 2800.0 ; to be used between R-R when one of the R beads is overmapping 5 carbons - consider if an alternative mapping is more appropiate! 39 | #define b_C1_C4_mid_5long 1 0.505 2800.0 40 | #define b_C4_C1_mid_5long 1 0.505 2800.0 ; symmetric, same as b_C1_C4_mid_5long 41 | #define b_C4_C4_mid_5long 1 0.490 2800.0 42 | ; bonds between a small 3 carbon bead and a regular 4 carbon bead: 43 | #define b_SC1_C1_mid 1 0.420 4400.0 ; to be used between S to R beads 44 | #define b_SC1_C4_mid 1 0.405 4400.0 45 | #define b_SC4_C1_mid 1 0.405 4400.0 ; symmetric to b_SC1_C4_mid 46 | #define b_SC4_C4_mid 1 0.390 4400.0 47 | #define b_SC1_C1_end 1 0.430 4400.0 ; at the end of the chain, internal conformations in AA reference results in a longer bond on average 48 | #define b_SC4_C1_end 1 0.415 4400.0 49 | #define b_SC1_C4_end 1 0.415 4400.0 50 | #define b_SC4_C4_end 1 0.400 4400.0 51 | 52 | [ angletypes ] 53 | ; name type angle k 54 | #define a_C1_C1_C1_def 1 180.0 13.5 ; can be used with CBT dihedral potential, fitted from charmm36 reference 55 | #define a_C1_C4_C1_def 1 140.0 10.0 ; one unsaturation 56 | 57 | #define a_C1_C1_C4_def 1 180.0 13.5 ; across a beads containing a double bond in the first/third bead 58 | #define a_C4_C1_C1_def 1 180.0 13.5 ; identical to a_C1_C1_C1 to improve transition temperatures of singly unsaturated lipids 59 | 60 | #define a_C1_C4_C4_def 1 135.0 8.0 ; second double bond results in different angle distribution 61 | #define a_C4_C4_C1_def 1 135.0 8.0 62 | 63 | #define a_C4_C1_C4_def 1 180.0 13.5 ; fitted from alkene 64 | 65 | #define a_C4_C4_C4_def 1 150.0 6.0 ; three double bonds in a row seem to sample a broader distribution of angles with a tendency for the third doube bond to point in the opposite direction 66 | 67 | ;;;;; 68 | ;;;;; Phospholipids 69 | ;;;;; 70 | ; section containing parameters for phospholipid head groups 71 | 72 | [ bondtypes ] 73 | ; default bonds between head group beads and phosphate to tails 74 | ; name type length k 75 | ;PC head group 76 | #define b_NC3_PO4_def 1 0.404 7000.0 77 | ;PE head group 78 | #define b_NH3_PO4_def 1 0.357 7000.0 79 | ;PG head group 80 | #define b_GL0_PO4_def 1 0.375 7000.0 81 | ;PS head group 82 | #define b_CNO_PO4_def 1 0.388 8000.0 83 | 84 | ;Phosphate to glycerol backbone and PA 85 | #define b_PO4_GL_def 1 0.440 1500.0 86 | #define b_PO4_GL_def_long 1 0.524 1200.0 87 | ;Phosphate to ether backbone and PA 88 | #define b_PO4_ET_def 1 0.440 1500.0 89 | #define b_PO4_ET_def_long 1 0.524 1200.0 90 | 91 | ; TAP to glycerol backbone 92 | #define a_NC3_GL_C_def 1 139.0 10.0 93 | 94 | ;bis(monoacylglycero) phosphate (2,2' isomer) 95 | #define b_GL_OH_22_bmp 1 0.292 6000.0 96 | 97 | ;bis(monoacylglycero) phosphate (3,3' isomer) 98 | #define b_PO4_OH_33_bmp 1 0.323 4000.0 99 | #define b_OH_GL_33_bmp 1 0.288 6000.0 100 | 101 | ;cardiolipin linker 102 | #define b_PO4_GL_cl 1 0.368 6000.0 103 | 104 | [ angletypes ] 105 | ; name type angle k 106 | ;PC head group 107 | #define a_NC3_PO4_GL_def 1 125.0 15.0 108 | #define a_NC3_PO4_ET_def 1 125.0 15.0 109 | ;PE head group 110 | #define a_NH3_PO4_GL_def 1 110.0 15.0 111 | #define a_NH3_PO4_ET_def 1 110.0 15.0 112 | ;PG head group 113 | #define a_GL0_PO4_GL_def 1 110.0 10.0 114 | #define a_GL0_PO4_ET_def 1 110.0 10.0 115 | ;PS head group 116 | #define a_CNO_PO4_GL_def 1 115.0 17.5 117 | #define a_CNO_PO4_ET_def 1 115.0 17.5 118 | ;2 bead PS HG 119 | #define a_PS1_PS2_PO4_def 1 125.0 100.0 120 | #define a_PS2_PO4_GL_def 1 110.0 10.0 121 | #define a_PS2_PO4_ET_def 1 110.0 10.0 122 | 123 | ;Phosphate to glycerol backbone and PA 124 | #define a_PO4_GL_C_def 1 139.0 10.0 125 | 126 | ;Phosphate to ether backbone 127 | #define a_PO4_ET_C_def 1 135.0 20.0 128 | 129 | ;bis(monoacylglycero) phosphate (2,2' isomer) 130 | #define a_PO4_GL_OH_22_bmp 1 70.0 8.0 131 | #define a_OH_GL_C_22_bmp 1 135.0 27.5 132 | 133 | ;bis(monoacylglycero) phosphate (3,3' isomer) 134 | #define a_PO4_OH_GL_33_bmp 6 130.0 0.0 0.0 -4.0 0.0 0.5 135 | #define a_OH_GL_C_33_bmp 1 130.0 25.0 136 | 137 | ;cardiolipin linker 138 | #define a_PO4_GL_PO4_cl 1 130.0 17.5 139 | #define a_GL_PO4_GL_cl 1 110.0 10.0 140 | 141 | 142 | ;;;;; 143 | ;;;;; Sphingomyelin and ceramide 144 | ;;;;; 145 | 146 | [ bondtypes ] 147 | ; name type length k 148 | #define b_PO4_OH1_sm 1 0.380 6000.0 149 | #define b_PO4_AM2_sm 1 0.490 6000.0 150 | #define b_OH1_AM2_sm 1 0.305 20000.0 151 | #define b_OH1_SC4_sm 1 0.345 20000.0 152 | #define b_AM2_SC1_sm 1 0.330 4000.0 153 | #define b_AM2_C1_sm_5long 1 0.405 2400.0 154 | 155 | #define b_COH_OH1_sm 1 0.253 20000.0 156 | #define b_COH_AM2_sm 1 0.306 20000.0 157 | 158 | [ angletypes ] 159 | ; name type angle k 160 | #define a_NC3_PO4_OH1_sm 1 122.0 15.0 161 | #define a_PO4_OH1_AM2_sm 1 91.0 80.0 162 | #define a_PO4_OH1_C_sm 1 175.0 15.0 163 | #define a_OH1_AM2_C_sm 1 150.0 45.0 164 | #define a_AM2_OH1_C_sm 1 85.0 60.0 165 | #define a_AM2_C1_C1_sm 1 180.0 13.5 166 | #define a_AM2_C1_C4_sm 1 180.0 13.5 167 | #define a_AM2_C4_C1_sm 1 140.0 10.0 168 | #define a_AM2_C4_C4_sm 1 135.0 8.0 169 | #define a_OH1_C1_C1_sm 1 180.0 13.5 ; trans double bond 170 | #define a_COH_OH1_C_cera 1 149.0 100.0 171 | 172 | 173 | ;;;;; 174 | ;;;;; GLYCEROL, MONOGLYCERIDES, DIGLYCERIDES, TRIGLYCERIDES 175 | ;;;;; 176 | ; section containing parameters for molecules containing glycerol moiety 177 | 178 | [ bondtypes ] 179 | ; default bond between GL beads in glycerol moieties (e.g. glycerophospholipid backbone) 180 | ; name type length k 181 | ; Below GL is an ester bead as SN4a in triglycerides glycerol backbone 182 | #define b_GL_GL_glyc 1 0.315 2100.0 ; in glycerol using SN4a beads 183 | #define b_GL_GL_glyc_long 1 0.395 3000.0 ; between sn1 and sn3 esters in triglycerides 184 | 185 | #define b_GL_C1_glyc_5long 1 0.450 2400.0 ; attaching glycerol+ester beads to hydrocarbon tails 186 | #define b_GL_C4_glyc_5long 1 0.435 2400.0 ; attaching glycerol+ester beads to hydrocarbon tail with immediate double bond e.g. 22:6 187 | ; These short bonds should only be used if the carbon bead is a small bead 188 | #define b_GL_SC1_glyc 1 0.375 4400.0 ; to distinguish shorter tail e.g. 16:0 from 18:0 189 | #define b_GL_SC4_glyc 1 0.360 4400.0 ; to distinguish shorter tail e.g. 16:0 from 18:0 190 | 191 | #define b_COH_GL_def 1 0.284 6000.0 ; alkohol in diacylglycerols 192 | #define b_COH_GL_def_long 1 0.362 8000.0 ; alkohol in diacylglycerols 193 | 194 | #define b_NC3_GL_def 1 0.450 3800.0 ; TAP trimethylammonium propane 195 | #define b_NC3_GL_def_long 1 0.524 1200.0 ; TAP trimethylammonium propane 196 | 197 | #define b_DOH_GL_def 1 0.313 4400.0 ; diol in monoglycerides 198 | 199 | [ angletypes ] 200 | ; name type angle k 201 | ; glycerol backbone to tail angle as in triglycerides and phospholipids 202 | #define a_GL_GL_C_glyc 1 120.0 20.0 ; glycerol backbone to tail angle 203 | #define a_GL_C1_C1_glyc 1 180.0 13.5 204 | #define a_GL_C1_C4_glyc 1 180.0 13.5 205 | #define a_GL_C4_C1_glyc 1 140.0 10.0 ; warning estimated from makeshift charmm36 parameters (the needed dihedral for this bond is not present in c36) 206 | #define a_GL_C4_C4_glyc 1 135.0 8.0 ; based on PDPC 207 | 208 | #define a_COH_GL_C_def 1 139.0 30.0 ; hydroxyl in diglycerides 209 | 210 | #define a_DOH_GL_C_def 1 132.0 14.0 ; diol in monoglycerides 211 | 212 | 213 | ;;;;; 214 | ;;;;; ETHERLIPIDS, PLASMALOGENS 215 | ;;;;; 216 | 217 | [ bondtypes ] 218 | ; name type length k 219 | #define b_ET_ET_ether 1 0.315 3200.0 ; di-alkyl 220 | #define b_GL_ET_plasm 1 0.315 3200.0 ; alkenyl-acyl (plasmalogens) 221 | #define b_ET_GL_plasm 1 0.315 3200.0 ; WARNING acyl-alkenyl (sn1/sn2) not validated 222 | 223 | #define b_ET_C1_ether_5long 1 0.420 2400.0 ; attaching ether linker beads to hydrocarbon tails 224 | #define b_ET_C4_ether_5long 1 0.405 2400.0 ; attaching ether linker beads to hydrocarbon tail with immediate double bond e.g. 22:6 225 | ; These short bonds should only be used if the carbon bead is a small bead 226 | #define b_ET_SC1_ether 1 0.345 4400.0 ; to distinguish shorter tail e.g. 16:0 from 18:0 227 | #define b_ET_SC4_ether 1 0.330 4400.0 ; to distinguish shorter tail e.g. 16:0 from 18:0 228 | 229 | #define b_ET_C1_plasm_5long 1 0.420 2400.0 ; warning, analog to b_ET_C1_ether_5long 230 | #define b_ET_C4_plasm_5long 1 0.405 2400.0 ; warning, analog to b_ET_C4_ether_5long 231 | #define b_ET_SC1_plasm 1 0.345 4400.0 ; warning, analog to b_ET_SC1_ether 232 | #define b_ET_SC4_plasm 1 0.330 4400.0 ; warning, analog to b_ET_SC4_ether 233 | #define b_GL_C1_plasm_5long 1 0.450 2400.0 ; warning, analog to b_GL_C1_glyc_5long 234 | #define b_GL_C4_plasm_5long 1 0.435 2400.0 ; warning, analog to b_GL_C4_glyc_5long 235 | #define b_GL_SC1_plasm 1 0.375 4400.0 ; warning, analog to b_GL_SC1_glyc 236 | #define b_GL_SC4_plasm 1 0.360 4400.0 ; warning, analog to b_GL_SC4_glyc 237 | 238 | [ angletypes ] 239 | ; name type angle k 240 | ; glycerol backbone to tail angle as in triglycerides and phospholipids 241 | #define a_ET_ET_C_ether 1 120.0 20.0 ; ether backbone to tail angle validated on DHPCE and DMPCE 242 | #define a_ET_C1_C1_ether 1 180.0 13.5 ; ether backbone to tail angle validated on DHPCE and DMPCE 243 | #define a_ET_C1_C4_ether 1 180.0 13.5 ; warning, analog to a_GL_C1_C4_glyc 244 | #define a_ET_C4_C1_ether 1 140.0 10.0 ; warning, analog to a_GL_C4_C1_glyc 245 | #define a_ET_C4_C4_ether 1 135.0 8.0 ; warning, analog to a_GL_C4_C4_glyc 246 | 247 | #define a_GL_ET_C_plasm 1 120.0 20.0 ; alkenyl-acyl plasmalogen backbone to tail angle validated on PLA18 (PC) 248 | #define a_ET_GL_C_plasm 1 120.0 20.0 ; WARNING acyl-alkenyl (sn1/sn2) not validated 249 | #define a_ET_C1_C1_plasm 1 180.0 13.5 ; warning, analog to a_ET_C1_C1_ether 250 | #define a_ET_C1_C4_plasm 1 180.0 13.5 ; warning, analog to a_GL_C1_C4_glyc 251 | #define a_ET_C4_C1_plasm 1 140.0 10.0 ; warning, analog to a_GL_C4_C1_glyc 252 | #define a_ET_C4_C4_plasm 1 135.0 8.0 ; warning, analog to a_GL_C4_C4_glyc 253 | #define a_GL_C1_C1_plasm 1 180.0 13.5 ; warning, analog to a_GL_C1_C1_glyc 254 | #define a_GL_C1_C4_plasm 1 180.0 13.5 ; warning, analog to a_GL_C1_C4_glyc 255 | #define a_GL_C4_C1_plasm 1 140.0 10.0 ; warning, analog to a_GL_C4_C1_glyc 256 | #define a_GL_C4_C4_plasm 1 135.0 8.0 ; warning, analog to a_GL_C4_C4_glyc 257 | 258 | 259 | ;;;;; 260 | ;;;;; Fatty Acids 261 | ;;;;; 262 | 263 | [ bondtypes ] 264 | ; name type length k 265 | #define b_COO_C1_fa_5long 1 0.400 2800.0 266 | #define b_COO_C4_fa_5long 1 0.385 2800.0 267 | #define b_COO_SC1_fa 1 0.325 4800.0 268 | #define b_COO_SC4_fa 1 0.310 4800.0 269 | 270 | [ angletypes ] 271 | ; name type angle k 272 | #define a_COO_C1_C1_fa 1 180.0 13.5 273 | #define a_COO_C1_C4_fa 1 180.0 13.5 274 | #define a_COO_C4_C1_fa 1 140.0 10.0 275 | #define a_COO_C4_C4_fa 1 135.0 8.0 276 | 277 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_triglycerides_v2.itp: -------------------------------------------------------------------------------- 1 | ; 2 | ; Collection with all triacylglycerols Martini 3 lipids 3 | ; 4 | ;;;;; MARTINI 3.0 - Triglycerides 5 | ;;;;; 6 | ; please cite: 7 | ; K.B. Pedersen et al., The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior*, 8 | ; ACS Central Science, 2025. doi: 10.1021/acscentsci.5c00755 9 | ; P.C.T. Souza et al., Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics*, 10 | ; Nature Methods, 2021. doi: 10.1038/s41592-021-01098-3 11 | ; last edit Jan-2025, Kasper 12 | ;;;;; 13 | 14 | ;;;;; 15 | ;;;;; Triolein 16 | ;;;;; TO 17 | ;;;;; 18 | 19 | ;;;;; BEAD-INDEX MAPPING 20 | ;;;;; topology description 21 | ; 22 | ; GL1-C1A-D2A-C3A-C4A 1-2-3-4-5 23 | ; | | 24 | ; GL2-C1B-D2B-C3B-C4B 6-7-8-9-10 25 | ; | | 26 | ; GL3-C1C-D2C-C3C-C4C 11-12-13-14-15 27 | ; 28 | 29 | [moleculetype] 30 | TO 1 31 | 32 | [atoms] 33 | ; id type resnr residu atom cgnr charge 34 | 1 SN4a 1 TO GL1 1 0 35 | 2 C1 1 TO C1A 2 0 ; 5-1 mapping 36 | 3 C4h 1 TO D2A 3 0 37 | 4 C1 1 TO C3A 4 0 38 | 5 C1 1 TO C4A 5 0 39 | 6 SN4a 1 TO GL2 6 0 40 | 7 C1 1 TO C1B 7 0 ; 5-1 mapping 41 | 8 C4h 1 TO D2B 8 0 42 | 9 C1 1 TO C3B 9 0 43 | 10 C1 1 TO C4B 10 0 44 | 11 SN4a 1 TO GL3 11 0 45 | 12 C1 1 TO C1C 12 0 ; 5-1 mapping 46 | 13 C4h 1 TO D2C 13 0 47 | 14 C1 1 TO C3C 14 0 48 | 15 C1 1 TO C4C 15 0 49 | 50 | [bonds] 51 | ; i j funct length force.c. 52 | 1 6 b_GL_GL_glyc ; backbone 53 | 6 11 b_GL_GL_glyc ; backbone 54 | 1 11 b_GL_GL_glyc_long ; backbone 55 | 1 2 b_GL_C1_glyc_5long ; glycerol+ester bead to hydrocarbon tail 56 | 2 3 b_C1_C4_mid_5long ; represents 5 atoms => longer bond 57 | 3 4 b_C4_C1_mid 58 | 4 5 b_C1_C1_end 59 | 6 7 b_GL_C1_glyc_5long 60 | 7 8 b_C1_C4_mid_5long 61 | 8 9 b_C4_C1_mid 62 | 9 10 b_C1_C1_end 63 | 11 12 b_GL_C1_glyc_5long 64 | 12 13 b_C1_C4_mid_5long 65 | 13 14 b_C4_C1_mid 66 | 14 15 b_C1_C1_end 67 | 68 | [angles] 69 | ; i j k 70 | 2 1 6 a_GL_GL_C_glyc ; backbone to tail 1 71 | 12 11 6 a_GL_GL_C_glyc ; backbone to tail 3 72 | 7 6 1 a_GL_GL_C_glyc ; backbone to tail 2 73 | 7 6 11 a_GL_GL_C_glyc ; backbone to tail 2 74 | ; tails attached to glycerol 75 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 76 | 2 3 4 a_C1_C4_C1_def ; cis double bond 77 | 3 4 5 a_C1_C1_C4_def 78 | 6 7 8 a_GL_C1_C1_glyc ; tail 2 79 | 7 8 9 a_C1_C4_C1_def ; cis double bond 80 | 8 9 10 a_C1_C1_C4_def 81 | 11 12 13 a_GL_C1_C1_glyc ; tail 3 82 | 12 13 14 a_C1_C4_C1_def ; cis double bond 83 | 13 14 15 a_C1_C1_C4_def 84 | 85 | ;;;;; 86 | ;;;;; Trilinolein 87 | ;;;;; TL 88 | ;;;;; 89 | 90 | ;;;;; BEAD-INDEX MAPPING 91 | ;;;;; topology description 92 | ; 93 | ; GL1-C1A-D2A-D3A-C4A 1-2-3-4-5 94 | ; | | 95 | ; GL2-C1B-D2B-D3B-C4B 6-7-8-9-10 96 | ; | | 97 | ; GL3-C1C-D2C-D3C-C4C 11-12-13-14-15 98 | 99 | [moleculetype] 100 | TL 1 101 | 102 | [atoms] 103 | ; id type resnr residu atom cgnr charge 104 | 1 SN4a 1 TL GL1 1 0 105 | 2 C1 1 TL C1A 2 0 106 | 3 C4h 1 TL D2A 3 0 107 | 4 C4h 1 TL D3A 4 0 108 | 5 C1 1 TL C4A 5 0 109 | 6 SN4a 1 TL GL2 6 0 110 | 7 C1 1 TL C1B 7 0 111 | 8 C4h 1 TL D2B 8 0 112 | 9 C4h 1 TL D3B 9 0 113 | 10 C1 1 TL C4B 10 0 114 | 11 SN4a 1 TL GL3 11 0 115 | 12 C1 1 TL C1C 12 0 116 | 13 C4h 1 TL D2C 13 0 117 | 14 C4h 1 TL D3C 14 0 118 | 15 C1 1 TL C4C 15 0 119 | 120 | [bonds] 121 | ; i j funct length force.c. 122 | 1 6 b_GL_GL_glyc ; backbone 123 | 6 11 b_GL_GL_glyc ; backbone 124 | 1 11 b_GL_GL_glyc_long ; backbone 125 | 1 2 b_GL_C1_glyc_5long ; glycerol+ester bead to hydrocarbon tail 126 | 2 3 b_C1_C4_mid_5long ; represents 5 atoms => longer bond 127 | 3 4 b_C4_C4_mid 128 | 4 5 b_C4_C1_end 129 | 6 7 b_GL_C1_glyc_5long 130 | 7 8 b_C1_C4_mid_5long 131 | 8 9 b_C4_C4_mid 132 | 9 10 b_C4_C1_end 133 | 11 12 b_GL_C1_glyc_5long 134 | 12 13 b_C1_C4_mid_5long 135 | 13 14 b_C4_C4_mid 136 | 14 15 b_C4_C1_end 137 | 138 | [angles] 139 | ; i j k 140 | 2 1 6 a_GL_GL_C_glyc ; backbone to tail 1 141 | 12 11 6 a_GL_GL_C_glyc ; backbone to tail 3 142 | 7 6 1 a_GL_GL_C_glyc ; backbone to tail 2 143 | 7 6 11 a_GL_GL_C_glyc ; backbone to tail 2 144 | ; tails attached to glycerol 145 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 146 | 2 3 4 a_C1_C4_C4_def 147 | 3 4 5 a_C4_C4_C1_def 148 | 6 7 8 a_GL_C1_C1_glyc ; tail 2 149 | 7 8 9 a_C1_C4_C4_def 150 | 8 9 10 a_C4_C4_C1_def 151 | 11 12 13 a_GL_C1_C1_glyc ; tail 3 152 | 12 13 14 a_C1_C4_C4_def 153 | 13 14 15 a_C4_C4_C1_def 154 | 155 | ;;;;; 156 | ;;;;; Trilinolenin (α-linolenic, omega-3) 157 | ;;;;; TLN 158 | ;;;;; 159 | 160 | ;;;;; BEAD-INDEX MAPPING 161 | ;;;;; topology description 162 | ;;;;; 163 | ; 164 | ; GL1-C1A-D2A-D3A-D4A 1-2-3-4-5 165 | ; | | 166 | ; GL2-C1B-D2B-D3B-D4B 6-7-8-9-10 167 | ; | | 168 | ; GL3-C1C-D2C-D3C-D4C 11-12-13-14-15 169 | 170 | [moleculetype] 171 | TLN 1 172 | 173 | [atoms] 174 | ; id type resnr residu atom cgnr charge 175 | 1 SN4a 1 TLN GL1 1 0 176 | 2 C1 1 TLN C1A 2 0 177 | 3 C4h 1 TLN D2A 3 0 178 | 4 C4h 1 TLN D3A 4 0 179 | 5 C4h 1 TLN D4A 5 0 180 | 6 SN4a 1 TLN GL2 6 0 181 | 7 C1 1 TLN C1B 7 0 182 | 8 C4h 1 TLN D2B 8 0 183 | 9 C4h 1 TLN D3B 9 0 184 | 10 C4h 1 TLN D4B 10 0 185 | 11 SN4a 1 TLN GL3 11 0 186 | 12 C1 1 TLN C1C 12 0 187 | 13 C4h 1 TLN D2C 13 0 188 | 14 C4h 1 TLN D3C 14 0 189 | 15 C4h 1 TLN D4C 15 0 190 | 191 | [bonds] 192 | ; i j funct length force.c. 193 | 1 6 b_GL_GL_glyc ; backbone 194 | 6 11 b_GL_GL_glyc ; backbone 195 | 1 11 b_GL_GL_glyc_long ; backbone 196 | 1 2 b_GL_C1_glyc_5long ; glycerol+ester bead to hydrocarbon tail 197 | 2 3 b_C1_C4_mid_5long ; represents 5 atoms => longer bond 198 | 3 4 b_C4_C4_mid 199 | 4 5 b_C4_C4_end 200 | 6 7 b_GL_C1_glyc_5long 201 | 7 8 b_C1_C4_mid_5long 202 | 8 9 b_C4_C4_mid 203 | 9 10 b_C4_C4_end 204 | 11 12 b_GL_C1_glyc_5long 205 | 12 13 b_C1_C4_mid_5long 206 | 13 14 b_C4_C4_mid 207 | 14 15 b_C4_C4_end 208 | 209 | [angles] 210 | ; i j k 211 | 2 1 6 a_GL_GL_C_glyc ; backbone to tail 1 212 | 12 11 6 a_GL_GL_C_glyc ; backbone to tail 3 213 | 7 6 1 a_GL_GL_C_glyc ; backbone to tail 2 214 | 7 6 11 a_GL_GL_C_glyc ; backbone to tail 2 215 | ; tails attached to glycerol 216 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 217 | 2 3 4 a_C1_C4_C4_def 218 | 3 4 5 a_C4_C4_C4_def 219 | 6 7 8 a_GL_C1_C1_glyc ; tail 2 220 | 7 8 9 a_C1_C4_C4_def 221 | 8 9 10 a_C4_C4_C4_def 222 | 11 12 13 a_GL_C1_C1_glyc ; tail 3 223 | 12 13 14 a_C1_C4_C4_def 224 | 13 14 15 a_C4_C4_C4_def 225 | 226 | ;;;;; 227 | ;;;;; Tristearin 228 | ;;;;; TS 229 | ;;;;; 230 | 231 | ;;;;; BEAD-INDEX MAPPING 232 | ;;;;; topology description 233 | ; 234 | ; GL1-C1A-C2A-C3A-C4A 1-2-3-4-5 235 | ; | | 236 | ; GL2-C1B-C2B-C3B-C4B 6-7-8-9-10 237 | ; | | 238 | ; GL3-C1C-C2C-C3C-C4C 11-12-13-14-15 239 | 240 | [moleculetype] 241 | TS 1 242 | 243 | [atoms] 244 | ; id type resnr residu atom cgnr charge 245 | 1 SN4a 1 TS GL1 1 0 246 | 2 C1 1 TS C1A 2 0 247 | 3 C1 1 TS C2A 3 0 248 | 4 C1 1 TS C3A 4 0 249 | 5 C1 1 TS C4A 5 0 250 | 6 SN4a 1 TS GL2 6 0 251 | 7 C1 1 TS C1B 7 0 252 | 8 C1 1 TS C2B 8 0 253 | 9 C1 1 TS C3B 9 0 254 | 10 C1 1 TS C4B 10 0 255 | 11 SN4a 1 TS GL3 11 0 256 | 12 C1 1 TS C1C 12 0 257 | 13 C1 1 TS C2C 13 0 258 | 14 C1 1 TS C3C 14 0 259 | 15 C1 1 TS C4C 15 0 260 | 261 | [bonds] 262 | ; i j funct length force.c. 263 | 1 6 b_GL_GL_glyc ; backbone 264 | 6 11 b_GL_GL_glyc ; backbone 265 | 1 11 b_GL_GL_glyc_long ; backbone 266 | 1 2 b_GL_C1_glyc_5long ; glycerol+ester bead to hydrocarbon tail 267 | 2 3 b_C1_C1_mid_5long ; represents 5 atoms => longer bond 268 | 3 4 b_C1_C1_mid 269 | 4 5 b_C1_C1_end 270 | 6 7 b_GL_C1_glyc_5long 271 | 7 8 b_C1_C1_mid_5long 272 | 8 9 b_C1_C1_mid 273 | 9 10 b_C1_C1_end 274 | 11 12 b_GL_C1_glyc_5long 275 | 12 13 b_C1_C1_mid_5long 276 | 13 14 b_C1_C1_mid 277 | 14 15 b_C1_C1_end 278 | 279 | [angles] 280 | ; i j k 281 | 2 1 6 a_GL_GL_C_glyc ; backbone to tail 1 282 | 12 11 6 a_GL_GL_C_glyc ; backbone to tail 3 283 | 7 6 1 a_GL_GL_C_glyc ; backbone to tail 2 284 | 7 6 11 a_GL_GL_C_glyc ; backbone to tail 2 285 | ; tails attached to glycerol 286 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 287 | 2 3 4 a_C1_C1_C1_def 288 | 3 4 5 a_C1_C1_C1_def 289 | 6 7 8 a_GL_C1_C1_glyc ; tail 2 290 | 7 8 9 a_C1_C1_C1_def 291 | 8 9 10 a_C1_C1_C1_def 292 | 11 12 13 a_GL_C1_C1_glyc ; tail 3 293 | 12 13 14 a_C1_C1_C1_def 294 | 13 14 15 a_C1_C1_C1_def 295 | 296 | ;;;;; 297 | ;;;;; Tripalmitin 298 | ;;;;; TP 299 | ;;;;; 300 | 301 | ;;;;; BEAD-INDEX MAPPING 302 | ;;;;; topology description 303 | ; 304 | ; GL1-C1A-C2A-C3A-C4A 1-2-3-4-5 305 | ; | | 306 | ; GL2-C1B-C2B-C3B-C4B 6-7-8-9-10 307 | ; | | 308 | ; GL3-C1C-C2C-C3C-C4C 11-12-13-14-15 309 | 310 | [moleculetype] 311 | TP 1 312 | 313 | [atoms] 314 | ; id type resnr residu atom cgnr charge 315 | 1 SN4a 1 TP GL1 1 0 316 | 2 SC1 1 TP C1A 2 0 317 | 3 C1 1 TP C2A 3 0 318 | 4 C1 1 TP C3A 4 0 319 | 5 C1 1 TP C4A 5 0 320 | 6 SN4a 1 TP GL2 6 0 321 | 7 SC1 1 TP C1B 7 0 322 | 8 C1 1 TP C2B 8 0 323 | 9 C1 1 TP C3B 9 0 324 | 10 C1 1 TP C4B 10 0 325 | 11 SN4a 1 TP GL3 11 0 326 | 12 SC1 1 TP C1C 12 0 327 | 13 C1 1 TP C2C 13 0 328 | 14 C1 1 TP C3C 14 0 329 | 15 C1 1 TP C4C 15 0 330 | 331 | [bonds] 332 | ; i j funct length force.c. 333 | 1 6 b_GL_GL_glyc ; backbone 334 | 6 11 b_GL_GL_glyc ; backbone 335 | 1 11 b_GL_GL_glyc_long ; backbone 336 | 1 2 b_GL_SC1_glyc ; glycerol+ester bead to hydrocarbon tail 337 | 2 3 b_SC1_C1_mid 338 | 3 4 b_C1_C1_mid 339 | 4 5 b_C1_C1_end 340 | 6 7 b_GL_SC1_glyc 341 | 7 8 b_SC1_C1_mid 342 | 8 9 b_C1_C1_mid 343 | 9 10 b_C1_C1_end 344 | 11 12 b_GL_SC1_glyc 345 | 12 13 b_SC1_C1_mid 346 | 13 14 b_C1_C1_mid 347 | 14 15 b_C1_C1_end 348 | 349 | [angles] 350 | ; i j k 351 | 2 1 6 a_GL_GL_C_glyc ; backbone to tail 1 352 | 12 11 6 a_GL_GL_C_glyc ; backbone to tail 3 353 | 7 6 1 a_GL_GL_C_glyc ; backbone to tail 2 354 | 7 6 11 a_GL_GL_C_glyc ; backbone to tail 2 355 | ; tails attached to glycerol 356 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 357 | 2 3 4 a_C1_C1_C1_def 358 | 3 4 5 a_C1_C1_C1_def 359 | 6 7 8 a_GL_C1_C1_glyc ; tail 2 360 | 7 8 9 a_C1_C1_C1_def 361 | 8 9 10 a_C1_C1_C1_def 362 | 11 12 13 a_GL_C1_C1_glyc ; tail 3 363 | 12 13 14 a_C1_C1_C1_def 364 | 13 14 15 a_C1_C1_C1_def 365 | 366 | ;;;;; 367 | ;;;;; Trimyristin 368 | ;;;;; TM 369 | ;;;;; 370 | 371 | ;;;;; BEAD-INDEX MAPPING 372 | ;;;;; topology description 373 | ; 374 | ; GL1-C1A-C2A-C3A 1-2-3-4 375 | ; | | 376 | ; GL2-C1B-C2B-C3B 5-6-7-8 377 | ; | | 378 | ; GL3-C1C-C2C-C3C 9-10-11-12 379 | 380 | [moleculetype] 381 | TM 1 382 | 383 | [atoms] 384 | ; id type resnr residu atom cgnr charge 385 | 1 SN4a 1 TM GL1 1 0 386 | 2 C1 1 TM C1A 2 0 387 | 3 C1 1 TM C2A 3 0 388 | 4 C1 1 TM C3A 4 0 389 | 5 SN4a 1 TM GL2 5 0 390 | 6 C1 1 TM C1B 6 0 391 | 7 C1 1 TM C2B 7 0 392 | 8 C1 1 TM C3B 8 0 393 | 9 SN4a 1 TM GL3 9 0 394 | 10 C1 1 TM C1C 10 0 395 | 11 C1 1 TM C2C 11 0 396 | 12 C1 1 TM C3C 12 0 397 | 398 | [bonds] 399 | ; i j funct length force.c. 400 | 1 5 b_GL_GL_glyc ; backbone 401 | 5 9 b_GL_GL_glyc ; backbone 402 | 1 9 b_GL_GL_glyc_long ; backbone 403 | 1 2 b_GL_C1_glyc_5long ; glycerol+ester bead to hydrocarbon tail 404 | 2 3 b_C1_C1_mid_5long ; represents 5 atoms => longer bond 405 | 3 4 b_C1_C1_end 406 | 5 6 b_GL_C1_glyc_5long 407 | 6 7 b_C1_C1_mid_5long 408 | 7 8 b_C1_C1_end 409 | 9 10 b_GL_C1_glyc_5long 410 | 10 11 b_C1_C1_mid_5long 411 | 11 12 b_C1_C1_end 412 | 413 | [angles] 414 | ; i j k 415 | 2 1 5 a_GL_GL_C_glyc ; backbone to tail 1 416 | 10 9 5 a_GL_GL_C_glyc ; backbone to tail 3 417 | 6 5 1 a_GL_GL_C_glyc ; backbone to tail 2 418 | 6 5 9 a_GL_GL_C_glyc ; backbone to tail 2 419 | ; tails attached to glycerol 420 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 421 | 2 3 4 a_C1_C1_C1_def 422 | 5 6 7 a_GL_C1_C1_glyc ; tail 2 423 | 6 7 8 a_C1_C1_C1_def 424 | 9 10 11 a_GL_C1_C1_glyc ; tail 3 425 | 10 11 12 a_C1_C1_C1_def 426 | 427 | ;;;;; 428 | ;;;;; Trilaurin 429 | ;;;;; TLA 430 | ;;;;; 431 | 432 | ;;;;; BEAD-INDEX MAPPING 433 | ;;;;; topology description 434 | ; 435 | ; GL1-C1A-C2A-C3A 1-2-3-4 436 | ; | | 437 | ; GL2-C1B-C2B-C3B 5-6-7-8 438 | ; | | 439 | ; GL3-C1C-C2C-C3C 9-10-11-12 440 | 441 | [moleculetype] 442 | TLA 1 443 | 444 | [atoms] 445 | ; id type resnr residu atom cgnr charge 446 | 1 SN4a 1 TLA GL1 1 0 447 | 2 SC1 1 TLA C1A 2 0 448 | 3 C1 1 TLA C2A 3 0 449 | 4 C1 1 TLA C3A 4 0 450 | 5 SN4a 1 TLA GL2 5 0 451 | 6 SC1 1 TLA C1B 6 0 452 | 7 C1 1 TLA C2B 7 0 453 | 8 C1 1 TLA C3B 8 0 454 | 9 SN4a 1 TLA GL3 9 0 455 | 10 SC1 1 TLA C1C 10 0 456 | 11 C1 1 TLA C2C 11 0 457 | 12 C1 1 TLA C3C 12 0 458 | 459 | [bonds] 460 | ; i j funct length force.c. 461 | 1 5 b_GL_GL_glyc ; backbone 462 | 5 9 b_GL_GL_glyc ; backbone 463 | 1 9 b_GL_GL_glyc_long ; backbone 464 | 1 2 b_GL_SC1_glyc ; glycerol+ester bead to hydrocarbon tail 465 | 2 3 b_SC1_C1_mid 466 | 3 4 b_C1_C1_end 467 | 5 6 b_GL_SC1_glyc 468 | 6 7 b_SC1_C1_mid 469 | 7 8 b_C1_C1_end 470 | 9 10 b_GL_SC1_glyc 471 | 10 11 b_SC1_C1_mid 472 | 11 12 b_C1_C1_end 473 | 474 | [angles] 475 | ; i j k 476 | 2 1 5 a_GL_GL_C_glyc ; backbone to tail 1 477 | 10 9 5 a_GL_GL_C_glyc ; backbone to tail 3 478 | 6 5 1 a_GL_GL_C_glyc ; backbone to tail 2 479 | 6 5 9 a_GL_GL_C_glyc ; backbone to tail 2 480 | ; tails attached to glycerol 481 | 1 2 3 a_GL_C1_C1_glyc ; tail 1 482 | 2 3 4 a_C1_C1_C1_def 483 | 5 6 7 a_GL_C1_C1_glyc ; tail 2 484 | 6 7 8 a_C1_C1_C1_def 485 | 9 10 11 a_GL_C1_C1_glyc ; tail 3 486 | 10 11 12 a_C1_C1_C1_def 487 | -------------------------------------------------------------------------------- /ITPs/martini_v3.0.0_solvents_v1.itp: -------------------------------------------------------------------------------- 1 | ;;;;; Martini 3 - Database of solvents 2 | ;;;;; 3 | ;;;;; File updated on 2021-03-29 4 | ;;;;; 5 | ;;;;; Version: 3.0.0_v1 6 | ;;;;; 7 | ;;;;; This collection contains the models included as part of the Martini 3 publication: 8 | ;;;;; PCT Souza, et al., Nat. Methods, 2021. DOI: 10.1038/s41592-021-01098-3 9 | 10 | ;;;;;; WATER (representing 4 molecules) 11 | 12 | [ moleculetype ] 13 | ; molname nrexcl 14 | W 1 15 | 16 | [ atoms ] 17 | ;id type resnr residu atom cgnr charge 18 | 1 W 1 W W 1 0 19 | 20 | ;;;;;;; DIMETHYLSULFOXIDE 21 | 22 | [ moleculetype ] 23 | ; molname nrexcl 24 | DMSO 1 25 | 26 | [atoms] 27 | ; id type resnr residu atom cgnr charge 28 | 1 SC6 1 DMS S1 1 0 29 | 2 TP6 1 DMS O2 2 0 30 | 31 | [bonds] 32 | ; i j funct length force.c. 33 | 1 2 1 0.300 8000 34 | 35 | ;;;;;;; ACETONITRILE 36 | 37 | [ moleculetype ] 38 | ; molname nrexcl 39 | ACN 1 40 | 41 | [ atoms ] 42 | ;id type resnr residu atom cgnr charge 43 | 1 SN5ah 1 ACN ACN 1 0 44 | 45 | ;;;;;;;;; ALKANES 46 | 47 | ;;;;;; HEXANE 48 | 49 | [moleculetype] 50 | ; molname nrexcl 51 | HEX 1 52 | 53 | [atoms] 54 | ; id type resnr residu atom cgnr charge 55 | 1 SC2 1 HEX C1 1 0 56 | 2 SC2 1 HEX C2 2 0 57 | 58 | [bonds] 59 | ; i j funct length force.c. 60 | 1 2 1 0.405 5000 61 | 62 | ;;;;;; OCTANE 63 | 64 | [moleculetype] 65 | ; molname nrexcl 66 | OCT 1 67 | 68 | [atoms] 69 | ; id type resnr residu atom cgnr charge 70 | 1 C1 1 OCT C1 1 0 71 | 2 C1 1 OCT C2 2 0 72 | 73 | [bonds] 74 | ; i j funct length force.c. 75 | 1 2 1 0.475 3800 76 | 77 | ;;;;;; DODECANE 78 | 79 | [moleculetype] 80 | ; molname nrexcl 81 | DOD 1 82 | 83 | [atoms] 84 | ; id type resnr residu atom cgnr charge 85 | 1 C1 1 DOD C1 1 0 86 | 2 C1 1 DOD C2 2 0 87 | 3 C1 1 DOD C3 3 0 88 | 89 | [bonds] 90 | ; i j funct length force.c. 91 | 1 2 1 0.475 3800 92 | 2 3 1 0.475 3800 93 | 94 | [angles] 95 | ; i j k funct angle force.c. 96 | 1 2 3 2 180.0 35.0 97 | 98 | ;;;;;; HEXADECANE 99 | 100 | [moleculetype] 101 | ; molname nrexcl 102 | HD 1 103 | 104 | [atoms] 105 | ; id type resnr residu atom cgnr charge 106 | 1 C1 1 HD C1 1 0 107 | 2 C1 1 HD C2 2 0 108 | 3 C1 1 HD C3 3 0 109 | 4 C1 1 HD C4 4 0 110 | 111 | [bonds] 112 | ; i j funct length force.c. 113 | 1 2 1 0.475 3800 114 | 2 3 1 0.47 3800 115 | 3 4 1 0.475 3800 116 | 117 | [angles] 118 | ; i j k funct angle force.c. 119 | 1 2 3 2 180.0 35.0 120 | 2 3 4 2 180.0 35.0 121 | 122 | ;;;;;;;;; ALKENES 123 | 124 | ;;;;;; 1-HEXENE 125 | 126 | [moleculetype] 127 | ; molname nrexcl 128 | HXE 1 129 | 130 | [atoms] 131 | ; id type resnr residu atom cgnr charge 132 | 1 SC4 1 HXE D1 1 0 133 | 2 SC2 1 HXE C2 2 0 134 | 135 | [bonds] 136 | ; i j funct length force.c. 137 | ; 1 2 1 0.360 5000 138 | 1 2 1 0.395 5000 139 | 140 | ;;;;;; 1-OCTENE 141 | 142 | [moleculetype] 143 | ; molname nrexcl 144 | OCE 1 145 | 146 | [atoms] 147 | ; id type resnr residu atom cgnr charge 148 | 1 C4 1 OCE D1 1 0 149 | 2 C1 1 OCE C2 2 0 150 | 151 | [bonds] 152 | ; i j funct length force.c. 153 | 1 2 1 0.470 3800 154 | 155 | ;;;;;; 1-DODECENE 156 | 157 | [moleculetype] 158 | ; molname nrexcl 159 | DOE 1 160 | 161 | [atoms] 162 | ; id type resnr residu atom cgnr charge 163 | 1 C4 1 DOE D1 1 0 164 | 2 C1 1 DOE C2 2 0 165 | 3 C1 1 DOE C3 3 0 166 | 167 | [bonds] 168 | ; i j funct length force.c. 169 | 1 2 1 0.470 3800 170 | 2 3 1 0.475 3800 171 | 172 | [angles] 173 | ; i j k funct angle force.c. 174 | 1 2 3 2 180.0 35.0 175 | 176 | ;;;;;;;;; ALKYNES 177 | 178 | ;;;;;; 1-HEXYNE 179 | 180 | [moleculetype] 181 | ; molname nrexcl 182 | HXY 1 183 | 184 | [atoms] 185 | ; id type resnr residu atom cgnr charge 186 | 1 SC6 1 HXY T1 1 0 187 | 2 SC2 1 HXY C2 2 0 188 | 189 | [bonds] 190 | ; i j funct length force.c. 191 | 1 2 1 0.390 5000 192 | 193 | ;;;;;; 1-OCTYNE 194 | 195 | [moleculetype] 196 | ; molname nrexcl 197 | OCY 1 198 | 199 | [atoms] 200 | ; id type resnr residu atom cgnr charge 201 | 1 C6 1 OCY T1 1 0 202 | 2 C1 1 OCY C2 2 0 203 | 204 | [bonds] 205 | ; i j funct length force.c. 206 | 1 2 1 0.468 3800 207 | 208 | ;;;;;;;;; DIENES 209 | 210 | ;;;;;; 1-4-HEXADIENE 211 | 212 | [moleculetype] 213 | ; molname nrexcl 214 | HXD14 1 215 | 216 | [atoms] 217 | ; id type resnr residu atom cgnr charge 218 | 1 SC4 1 HXD D1 1 0 219 | 2 SC4 1 HXD D2 2 0 220 | 221 | [bonds] 222 | ; i j funct length force.c. 223 | 1 2 1 0.385 5000 224 | 225 | ;;;;;; 9-12 OCTADECADIENE 226 | 227 | [moleculetype] 228 | ; molname nrexcl 229 | OCD912 1 230 | 231 | [atoms] 232 | ; id type resnr residu atom cgnr charge 233 | 1 C1h 1 OCD C1 1 0 234 | 2 C5h 1 OCD C2 2 0 235 | 3 C5h 1 OCD C3 3 0 236 | 4 C1h 1 OCD C4 4 0 237 | 238 | [bonds] 239 | ; i j funct length force.c. 240 | 1 2 1 0.49 3800 241 | 2 3 1 0.49 3800 242 | 3 4 1 0.49 3800 243 | 244 | [angles] 245 | ; i j k funct angle force.c. 246 | 1 2 3 2 100.0 10.0 247 | 2 3 4 2 100.0 10.0 248 | 249 | ;;;;;;;;; HALOALKANES 250 | 251 | ;;;;;; 1,2 DICHLOROETHANE 252 | 253 | [moleculetype] 254 | ; molname nrexcl 255 | DCE 1 256 | 257 | [atoms] 258 | ; id type resnr residu atom cgnr charge 259 | 1 X3h 1 DCE CX 1 0 260 | 261 | ;;;;;; CHLOROFORM 262 | 263 | [moleculetype] 264 | ; molname nrexcl 265 | CLF 1 266 | 267 | [atoms] 268 | ; id type resnr residu atom cgnr charge 269 | 1 X2 1 CLF CX 1 0 270 | 271 | ;;;;;; TETRACHLOROMETHANE 272 | 273 | [moleculetype] 274 | ; molname nrexcl 275 | TCM 1 276 | 277 | [atoms] 278 | ; id type resnr residu atom cgnr charge 279 | 1 X1 1 TCM CX 1 0 280 | 281 | ;;;;;; TRICHLOROETHYLENE 282 | 283 | [moleculetype] 284 | ; molname nrexcl 285 | TCE 1 286 | 287 | [atoms] 288 | ; id type resnr residu atom cgnr charge 289 | 1 X3h 1 TCE CX 1 0 290 | 291 | ;;;;;; 2,2,2-TRIFLUOROETHANOL 292 | 293 | [moleculetype] 294 | ; molname nrexcl 295 | TFEOL 1 296 | 297 | [atoms] 298 | ; id type resnr residu atom cgnr charge 299 | 1 TP1d 1 TFE CO 1 0 ; 300 | 2 SX4e 1 TFE CX 2 0 ; 301 | 302 | [bonds] 303 | ; i j funct length force.c. 304 | 1 2 1 0.300 5000 305 | 306 | ;;;;;;;;; ALCOOLS 307 | 308 | ;;;;;; METHANOL (representing 2 molecules) 309 | 310 | [ moleculetype ] 311 | ; molname nrexcl 312 | MEO 1 313 | 314 | [ atoms ] 315 | ;id type resnr residu atom cgnr charge 316 | 1 SP2r 1 MEO MEO 1 0 317 | 318 | ;;;;;; ETHANOL 319 | 320 | [ moleculetype ] 321 | ; molname nrexcl 322 | ETO 1 323 | 324 | [ atoms ] 325 | ;id type resnr residu atom cgnr charge 326 | 1 SP1 1 ETO ETO 1 0 327 | 328 | ;;;;;; ISOPROPANOL 329 | 330 | [ moleculetype ] 331 | ; molname nrexcl 332 | IPO 1 333 | 334 | [ atoms ] 335 | ;id type resnr residu atom cgnr charge 336 | 1 P1 1 IPO IPO 1 0 337 | 338 | ;;;;;; 1-PROPANOL 339 | 340 | [ moleculetype ] 341 | ; molname nrexcl 342 | PRO 1 343 | 344 | [ atoms ] 345 | ;id type resnr residu atom cgnr charge 346 | 1 N6 1 PRO PRO 1 0 347 | 348 | ;;;;;; 1-BUTANOL 349 | 350 | [moleculetype] 351 | ; molname nrexcl 352 | BTO 1 353 | 354 | [atoms] 355 | ; id type resnr residu atom cgnr charge 356 | 1 TC2 1 BTO C1 1 0 357 | 2 SP1 1 BTO O2 2 0 358 | 359 | [bonds] 360 | ; i j funct length force.c. 361 | 1 2 1 0.310 7000 ; 362 | 363 | ;;;;;; 1-HEXANOL 364 | 365 | [moleculetype] 366 | ; molname nrexcl 367 | HXO 1 368 | 369 | [atoms] 370 | ; id type resnr residu atom cgnr charge 371 | 1 C1 1 HXO C1 1 0 372 | 2 SP1 1 HXO R2 2 0 373 | 374 | [bonds] 375 | ; i j funct length force.c. 376 | 1 2 1 0.385 7000 ; 377 | 378 | ;;;;;; 1-HEPTANOL 379 | 380 | [moleculetype] 381 | ; molname nrexcl 382 | HPO 1 383 | 384 | [atoms] 385 | ; id type resnr residu atom cgnr charge 386 | 1 C1 1 HPO C1 1 0 387 | 2 P1 1 HPO R2 2 0 388 | 389 | [bonds] 390 | ; i j funct length force.c. 391 | 1 2 1 0.460 7000 ; 392 | 393 | ;;;;;; 1-OCTANOL 394 | 395 | [moleculetype] 396 | ; molname nrexcl 397 | OCO 1 398 | 399 | [atoms] 400 | ; id type resnr residu atom cgnr charge 401 | 1 SC2 1 OCO C1 1 0 402 | 2 SC2 1 OCO C2 2 0 403 | 3 SP1 1 OCO PC 3 0 404 | 405 | [bonds] 406 | ; i j funct length force.c. 407 | ; 1 2 1 0.366 5000 408 | ; 2 3 1 0.355 5000 409 | 1 2 1 0.390 5000 410 | 2 3 1 0.350 5000 411 | 412 | [angles] 413 | 1 2 3 2 150.0 100.0 414 | 415 | ;;;;;;;;; ETHERS 416 | 417 | ;;;;;; DIETHYL ETHER 418 | 419 | [moleculetype] 420 | ; molname nrexcl 421 | ETH 1 422 | 423 | [atoms] 424 | ; id type resnr residu atom cgnr charge 425 | 1 N2 1 ETH CO 1 0 426 | 427 | ;;;;;; DIISOPROPYL ETHER 428 | 429 | [moleculetype] 430 | ; molname nrexcl 431 | DISH 1 432 | 433 | [atoms] 434 | ; id type resnr residu atom cgnr charge 435 | 1 TC3 1 DISH C1 1 0 436 | 2 SN3ar 1 DISH O2 2 0 437 | 3 TC3 1 DISH C3 3 0 438 | 439 | [bonds] 440 | 441 | ; i j funct length force.c. 442 | 1 2 1 0.355 5000 443 | 2 3 1 0.355 5000 444 | 445 | [angles] 446 | 1 2 3 2 135.00 30 447 | 448 | ;;;;;; DIMETHOXYETHANE (OR GLYME) 449 | 450 | [moleculetype] 451 | ; molname nrexcl 452 | DXE 1 453 | 454 | [atoms] 455 | ; id type resnr residu atom cgnr charge 456 | 1 SN3ar 1 DXE R1 1 0 457 | 2 SN3ar 1 DXE R2 2 0 458 | 459 | [bonds] 460 | ; i j funct length force.c. 461 | 1 2 1 0.330 7000 ; 462 | 463 | ;;;;;; TRIGLYME 464 | 465 | [moleculetype] 466 | ; molname nrexcl 467 | TXE 1 468 | 469 | [atoms] 470 | ; id type resnr residu atom cgnr charge 471 | 1 SN3ar 1 TXE R1 1 0 472 | 2 SN3ar 1 TXE R2 2 0 473 | 3 SN3ar 1 TXE R2 3 0 474 | 475 | [bonds] 476 | ; i j funct length force.c. 477 | 1 2 1 0.330 7000 ; 478 | 2 3 1 0.330 7000 ; 479 | 480 | [angles] 481 | 1 2 3 10 135.00 15 482 | 1 2 3 2 135.00 5 483 | 484 | ;;;;;;;;; SULFIDES 485 | 486 | ;;;;;; DIISOPROPYL SULFIDE 487 | 488 | [moleculetype] 489 | ; molname nrexcl 490 | DISS 1 491 | 492 | [atoms] 493 | ; id type resnr residu atom cgnr charge 494 | 1 TC3 1 DISS C1 1 0 495 | 2 SC6 1 DISS S2 2 0 496 | 3 TC3 1 DISS C3 3 0 497 | 498 | [bonds] 499 | 500 | ; i j funct length force.c. 501 | 1 2 1 0.360 5000 502 | 2 3 1 0.360 5000 503 | 504 | [angles] 505 | 1 2 3 2 135.00 30 506 | 507 | ;;;;;;;;; KETONES 508 | 509 | ;;;;;; ACETONE 510 | 511 | [moleculetype] 512 | ; molname nrexcl 513 | PPN 1 514 | 515 | [atoms] 516 | ; id type resnr residu atom cgnr charge 517 | 1 N5a 1 PPN CO 1 0 518 | 519 | ;;;;;; BUTANONE 520 | 521 | [moleculetype] 522 | ; molname nrexcl 523 | BTN 1 524 | 525 | [atoms] 526 | ; id type resnr residu atom cgnr charge 527 | 1 N4ah 1 BTN CO 1 0 528 | 529 | ;;;;;; ACETYLACETONE 530 | 531 | [moleculetype] 532 | ; molname nrexcl 533 | ANN 1 534 | 535 | [atoms] 536 | ; id type resnr residu atom cgnr charge 537 | 1 SN5a 1 ANN R1 1 0 538 | 2 SN5a 1 ANN R2 2 0 539 | 540 | [bonds] 541 | ; i j funct length force.c. 542 | 1 2 1 0.350 7000 ; 543 | 544 | ;;;;;; HEXA-2-ONE 545 | 546 | [moleculetype] 547 | ; molname nrexcl 548 | HXN 1 549 | 550 | [atoms] 551 | ; id type resnr residu atom cgnr charge 552 | 1 C2 1 HXN C1 1 0 553 | 2 SN6a 1 HXN R2 2 0 554 | 555 | [bonds] 556 | ; i j funct length force.c. 557 | 1 2 1 0.380 7000 ; 558 | 559 | ;;;;;; HEPTA-2-ONE 560 | 561 | [moleculetype] 562 | ; molname nrexcl 563 | HPN 1 564 | 565 | [atoms] 566 | ; id type resnr residu atom cgnr charge 567 | 1 C2 1 HPN C1 1 0 568 | 2 N6a 1 HPN R2 2 0 569 | 570 | [bonds] 571 | ; i j funct length force.c. 572 | 1 2 1 0.450 7000 ; 573 | 574 | ;;;;;;;;; ALDEHYDES 575 | 576 | ;;;;;; BUTANAL 577 | 578 | [moleculetype] 579 | ; molname nrexcl 580 | BTA 1 581 | 582 | [atoms] 583 | ; id type resnr residu atom cgnr charge 584 | 1 TC3 1 BTA C1 1 0 585 | 2 SN6a 1 BTA N2 2 0 586 | 587 | [bonds] 588 | ; i j funct length force.c. 589 | 1 2 1 0.310 7000 ; 590 | 591 | ;;;;;; HEXANAL 592 | 593 | [moleculetype] 594 | ; molname nrexcl 595 | HXA 1 596 | 597 | [atoms] 598 | ; id type resnr residu atom cgnr charge 599 | 1 C1 1 HXA C1 1 0 600 | 2 SN6a 1 HXA R2 2 0 601 | 602 | [bonds] 603 | ; i j funct length force.c. 604 | 1 2 1 0.385 7000 ; 605 | 606 | ;;;;;; HEPTANAL 607 | 608 | [moleculetype] 609 | ; molname nrexcl 610 | HPA 1 611 | 612 | [atoms] 613 | ; id type resnr residu atom cgnr charge 614 | 1 C1 1 HPA C1 1 0 615 | 2 N6a 1 HPA R2 2 0 616 | 617 | [bonds] 618 | ; i j funct length force.c. 619 | 1 2 1 0.455 7000 ; 620 | 621 | ;;;;;;;;; ESTERS 622 | 623 | ;;;;;; METHYL ACETATE 624 | 625 | [moleculetype] 626 | ; molname nrexcl 627 | MEA 1 628 | 629 | [atoms] 630 | ; id type resnr residu atom cgnr charge 631 | 1 N4a 1 MEA CO 1 0 632 | 633 | ;;;;;; ETHYL ACETATE 634 | 635 | [moleculetype] 636 | ; molname nrexcl 637 | ETA 1 638 | 639 | [atoms] 640 | ; id type resnr residu atom cgnr charge 641 | 1 TC3 1 ETA R1 1 0 642 | 2 SN4a 1 ETA R2 2 0 643 | 644 | [bonds] 645 | ; i j funct length force.c. 646 | 1 2 1 0.310 7000 ; 647 | 648 | ;;;;;; ISO-BUTYL ACETATE 649 | 650 | [moleculetype] 651 | ; molname nrexcl 652 | IBA 1 653 | 654 | [atoms] 655 | ; id type resnr residu atom cgnr charge 656 | 1 SC2 1 IBA R1 1 0 657 | 2 SN4a 1 IBA R2 2 0 658 | 659 | [bonds] 660 | ; i j funct length force.c. 661 | 1 2 1 0.375 3500 ; 662 | 663 | ;;;;;; T-BUTYL ACETATE 664 | 665 | [moleculetype] 666 | ; molname nrexcl 667 | TBA 1 668 | 669 | [atoms] 670 | ; id type resnr residu atom cgnr charge 671 | 1 SC2 1 TBA R1 1 0 672 | 2 SN4a 1 TBA R2 2 0 673 | 674 | [bonds] 675 | ; i j funct length force.c. 676 | 1 2 1 0.376 7000 ; 677 | 678 | ;;;;;; N-BUTYL ACETATE 679 | 680 | [moleculetype] 681 | ; molname nrexcl 682 | NBA 1 683 | 684 | [atoms] 685 | ; id type resnr residu atom cgnr charge 686 | 1 C2 1 NBA R1 1 0 687 | 2 SN4a 1 NBA R2 2 0 688 | 689 | [bonds] 690 | ; i j funct length force.c. 691 | 1 2 1 0.405 7000 ; 692 | 693 | ;;;;;;;;; AMINES 694 | 695 | ;;;;;; DIETHYLAMINE 696 | 697 | [moleculetype] 698 | ; molname nrexcl 699 | DEI 1 700 | 701 | [atoms] 702 | ; id type resnr residu atom cgnr charge 703 | 1 N3r 1 DEI N1 1 0 704 | 705 | ;;;;;; TRIMETHYLAMINE 706 | 707 | [moleculetype] 708 | ; molname nrexcl 709 | TMI 1 710 | 711 | [atoms] 712 | ; id type resnr residu atom cgnr charge 713 | 1 SN3a 1 TMI N1 1 0 714 | 715 | ;;;;;; PROPYLAMINE 716 | 717 | [moleculetype] 718 | ; molname nrexcl 719 | PPI 1 720 | 721 | [atoms] 722 | ; id type resnr residu atom cgnr charge 723 | 1 N6d 1 PPI N1 1 0 724 | 725 | ;;;;;; DIMETHYLETHYLAMINE 726 | 727 | [moleculetype] 728 | ; molname nrexcl 729 | NDI 1 730 | 731 | [atoms] 732 | ; id type resnr residu atom cgnr charge 733 | 1 SN3 1 NDI N1 1 0 734 | 735 | ;;;;;; 1-BUTYLAMINE 736 | 737 | [moleculetype] 738 | ; molname nrexcl 739 | BTI 1 740 | 741 | [atoms] 742 | ; id type resnr residu atom cgnr charge 743 | 1 TC2 1 BTI C1 1 0 744 | 2 SN6d 1 BTI N2 2 0 745 | 746 | [bonds] 747 | ; i j funct length force.c. 748 | 1 2 1 0.310 7000 ; 749 | 750 | ;;;;;; 1-PENTYLAMINE 751 | 752 | [moleculetype] 753 | ; molname nrexcl 754 | PTI 1 755 | 756 | [atoms] 757 | ; id type resnr residu atom cgnr charge 758 | 1 SC2 1 PTI C1 1 0 759 | 2 SN6d 1 PTI N2 2 0 760 | 761 | [bonds] 762 | ; i j funct length force.c. 763 | 1 2 1 0.340 7000 ; 764 | 765 | ;;;;;; 1-HEXYLAMINE 766 | 767 | [moleculetype] 768 | ; molname nrexcl 769 | HXI 1 770 | 771 | [atoms] 772 | ; id type resnr residu atom cgnr charge 773 | 1 C1 1 HXI C1 1 0 774 | 2 SN6d 1 HXI N2 2 0 775 | 776 | [bonds] 777 | ; i j funct length force.c. 778 | 1 2 1 0.385 7000 ; 779 | 780 | ;;;;;; 1-HEPTYLAMINE 781 | 782 | [moleculetype] 783 | ; molname nrexcl 784 | HPI 1 785 | 786 | [atoms] 787 | ; id type resnr residu atom cgnr charge 788 | 1 C1 1 HPI C1 1 0 789 | 2 N6d 1 HPI N2 2 0 790 | 791 | [bonds] 792 | ; i j funct length force.c. 793 | 1 2 1 0.460 7000 ; 794 | 795 | ;;;;;; 1-OCTYLAMINE 796 | 797 | [moleculetype] 798 | ; molname nrexcl 799 | OCI 1 800 | 801 | [atoms] 802 | ; id type resnr residu atom cgnr charge 803 | 1 SC2 1 OCI C1 1 0 804 | 2 SC2 1 OCI C2 2 0 805 | 3 SN6d 1 OCI NC 3 0 806 | 807 | [bonds] 808 | ; i j funct length force.c. 809 | ; 1 2 1 0.366 5000 810 | ; 2 3 1 0.355 5000 811 | 1 2 1 0.390 5000 812 | 2 3 1 0.350 5000 813 | 814 | [angles] 815 | 1 2 3 2 150.0 100.0 816 | 817 | ;;;;;;;;; CARBOXYLIC ACIDS 818 | 819 | ;;;;;; ACETIC ACID 820 | 821 | [moleculetype] 822 | ; molname nrexcl 823 | ACAC 1 824 | 825 | [atoms] 826 | ; id type resnr residu atom cgnr charge 827 | 1 SP2 1 ACAC CO 1 0 828 | 829 | ;;;;;; PROPANOIC ACID 830 | 831 | [moleculetype] 832 | ; molname nrexcl 833 | PRAC 1 834 | 835 | [atoms] 836 | ; id type resnr residu atom cgnr charge 837 | 1 P2 1 PRAC CO 1 0 838 | 839 | ;;;;;;;;; AMIDES 840 | 841 | ;;;;;; DIMETHYLFORMAMIDE 842 | 843 | [moleculetype] 844 | ; molname nrexcl 845 | DMFD 1 846 | 847 | [atoms] 848 | ; id type resnr residu atom cgnr charge 849 | 1 P3a 1 DMF CNO 1 0 850 | 851 | ;;;;;; DIMETHYLACETAMIDE 852 | 853 | [moleculetype] 854 | ; molname nrexcl 855 | DMAD 1 856 | 857 | [atoms] 858 | ; id type resnr residu atom cgnr charge 859 | 1 P2ah 1 DMA CNO 1 0 860 | --------------------------------------------------------------------------------