├── LICENSE ├── README.md ├── figures ├── 1AKI_1box.png ├── 1AKI_boxes.png ├── 1AKI_solv_ions.png ├── 3htb_jz4_zoom.png ├── 3htb_t0_rewrap.png ├── 3htb_unit_cell.png ├── DPPC.png ├── DPPC_new_label.png ├── biphasic_system.png ├── biphasic_system_newbox.png ├── dG.tiff ├── free_energy_methane_water.png ├── free_energy_plot_bar.png ├── free_energy_plot_barint.png ├── jz4.png ├── kalp15_dppc.png ├── kalp_dppc_lipid_pack.png ├── kalp_dppc_water_deletor.png ├── kalp_membrane_with_planes.png ├── kalp_membrane_with_planes2.png ├── lysozyme_1aki.png ├── lysozyme_complex_3htb.png ├── peptide_chx.png ├── plot_kalp_dppc_Scd ├── plot_kalp_dppc_Scd.png ├── plot_kalp_dppc_density.png ├── plot_lyso_em_potential ├── plot_lyso_em_potential.png ├── plot_lyso_md_rg ├── plot_lyso_md_rg.png ├── plot_lyso_md_rmsd ├── plot_lyso_md_rmsd.png ├── plot_lyso_npt_density ├── plot_lyso_npt_density.png ├── plot_lyso_npt_pressure ├── plot_lyso_npt_pressure.png ├── plot_lyso_nvt_temperature ├── plot_lyso_nvt_temperature.png ├── umbrella_composite_pmf_histo.png ├── umbrella_pmf_shift.png ├── umbrella_protofibril_box.png ├── umbrella_protofibril_dissociate.png ├── umbrella_pullf_vs_pullx ├── umbrella_pullf_vs_pullx.png ├── umbrella_schematic2.png ├── umbrella_smd_pullf.png ├── vsites_co2.png ├── vsites_masses.png └── vsites_triatomic.png ├── gmx-tutorials-refs.bib ├── gmx_tutorials.pdf ├── gmx_tutorials.tex ├── information_for_authors.md ├── livecoms.cls ├── releases ├── LiveCoMS_Article_ASAP_V1.pdf ├── LiveCoMS_Article_V1.pdf └── header_V1.png ├── tutorial-files ├── README ├── biphasic │ ├── chx.gro │ ├── chx.top │ └── chx_10ns.gro ├── complex │ ├── 3HTB_clean.pdb │ ├── em.mdp │ ├── gromos54a7_atb.ff.tar.gz │ ├── ions.mdp │ ├── jz4.mol2 │ ├── jz4.pdb │ ├── jz4.str │ ├── jz4_UA.pdb │ ├── jz4_UA_gromos54a7.itp │ ├── jz4_allH.mol2 │ ├── jz4_allH.pdb │ ├── jz4_ini.pdb │ ├── md.mdp │ ├── npt.mdp │ ├── nvt.mdp │ └── sort_mol2_bonds.pl ├── free_energy │ ├── em_steep.mdp │ ├── job.sh │ ├── md.mdp │ ├── mdout.mdp │ ├── methane_water.gro │ ├── methane_water.pdb │ ├── npt.mdp │ ├── nvt.mdp │ ├── test.tpr │ ├── topol.top │ └── write_mdp.pl ├── lysozyme │ ├── ions.mdp │ ├── md.mdp │ ├── minim.mdp │ ├── npt.mdp │ └── nvt.mdp ├── membrane_protein │ ├── KALP-15_princ.pdb │ ├── anneal_npt.mdp │ ├── inflategro.pl │ ├── ions.mdp │ ├── kalp15-dppc.pdb │ ├── lipid_posre.itp │ ├── md.mdp │ ├── minim.mdp │ ├── minim_inflategro.mdp │ ├── npt.mdp │ ├── nvt.mdp │ ├── run_inflategro.sh │ ├── topol_dppc.top │ ├── topol_dppc_old.top │ └── water_deletor.pl ├── umbrella │ ├── 2BEG_model1_capped.pdb │ ├── get_distances.sh │ ├── ions.mdp │ ├── md_pull.mdp │ ├── md_umbrella.mdp │ ├── minim.mdp │ ├── npt.mdp │ ├── npt_umbrella.mdp │ └── setup-umbrella-script.tar.gz └── vsites │ ├── co2.pdb │ ├── em.mdp │ ├── md.mdp │ └── topol.top └── vancouver-livecoms.bst /README.md: -------------------------------------------------------------------------------- 1 | # From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package 2 | 3 | This document contains a description of seven tutorials for carrying out different types 4 | of molecular dynamics (MD) simulations in the popular, open-source GROMACS package. 5 | 6 | ## List of Authors 7 | 8 | - Justin A. Lemkul, Virginia Tech, Blacksburg, VA, USA 9 | 10 | ## List of Contributors 11 | 12 | 13 | ## Paper writing as code development 14 | 15 | This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay ["Paper writing as code development"](https://livecomsjournal.github.io/about/paper_code/). If you have comments or suggestions, we welcome them! Please [submit them as issues](https://guides.github.com/features/issues/) to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed [via pull requests](https://help.github.com/articles/about-pull-requests/). 16 | 17 | ## List of Released Versions 18 | 19 | - v1.0: Submitted to LiveCoMS 20 | 21 | ## Changelog 22 | 23 | - 5 March 2018: Started document 24 | - 10 July 2018: First full draft completed, all tutorials updated for GROMACS-2018 25 | - 27 August 2018: Revised based on peer review comments 26 | - 10 September 2018: Revised based on editorial comments 27 | - 30 December 2018: Final version of PDF and article files for publication in LiveCoMS 28 | - 2 January 2019: Final formatting fixes 29 | -------------------------------------------------------------------------------- /figures/1AKI_1box.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/figures/1AKI_1box.png 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505 | 58.5 1019.023 506 | 59.5 1018.9811 507 | 60.5 1019.4489 508 | 61.5 1019.2353 509 | 62.5 1019.612 510 | 63.5 1019.4916 511 | 64.5 1019.7593 512 | 65.5 1019.803 513 | 66.5 1020.0053 514 | 67.5 1020.0477 515 | 68.5 1020.4089 516 | 69.5 1020.3425 517 | 70.5 1020.5951 518 | 71.5 1020.2928 519 | 72.5 1019.4017 520 | 73.5 1019.1978 521 | 74.5 1019.0742 522 | 75.5 1019.1581 523 | 76.5 1019.1994 524 | 77.5 1019.5323 525 | 78.5 1019.0582 526 | 79.5 1019.0859 527 | 80.5 1019.2777 528 | 81.5 1019.482 529 | 82.5 1019.6404 530 | 83.5 1019.1781 531 | 84.5 1018.771 532 | 85.5 1018.8187 533 | 86.5 1018.6465 534 | 87.5 1019.0164 535 | 88.5 1019.5122 536 | 89.5 1019.2847 537 | 90.5 1019.1133 538 | 91.5 1019.2703 539 | 92.5 1019.5702 540 | 93.5 1020.1166 541 | 94.5 1020.0003 542 | 95.5 1019.4734 543 | & 544 | -------------------------------------------------------------------------------- /figures/plot_lyso_npt_density.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/figures/plot_lyso_npt_density.png -------------------------------------------------------------------------------- /figures/plot_lyso_npt_pressure: -------------------------------------------------------------------------------- 1 | # Grace project file 2 | # 3 | @version 50125 4 | @page size 792, 612 5 | @page scroll 5% 6 | @page inout 5% 7 | @link page off 8 | @map font 0 to "Times-Roman", "Times-Roman" 9 | @map font 1 to "Times-Italic", "Times-Italic" 10 | @map font 2 to "Times-Bold", "Times-Bold" 11 | @map font 3 to "Times-BoldItalic", "Times-BoldItalic" 12 | @map font 4 to "Helvetica", "Helvetica" 13 | @map font 5 to "Helvetica-Oblique", "Helvetica-Oblique" 14 | @map font 6 to "Helvetica-Bold", "Helvetica-Bold" 15 | @map font 7 to "Helvetica-BoldOblique", "Helvetica-BoldOblique" 16 | @map font 8 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-100.61191 501 | 54.5 -111.9701 502 | 55.5 -86.156065 503 | 56.5 -99.008617 504 | 57.5 -80.393145 505 | 58.5 -117.43577 506 | 59.5 -98.306826 507 | 60.5 -60.410955 508 | 61.5 -49.975632 509 | 62.5 -39.756969 510 | 63.5 -34.895492 511 | 64.5 18.056585 512 | 65.5 11.487612 513 | 66.5 26.838609 514 | 67.5 71.196233 515 | 68.5 70.280104 516 | 69.5 59.572456 517 | 70.5 64.289143 518 | 71.5 62.064813 519 | 72.5 29.387877 520 | 73.5 31.797034 521 | 74.5 34.849022 522 | 75.5 53.79745 523 | 76.5 57.156047 524 | 77.5 15.968558 525 | 78.5 43.060205 526 | 79.5 52.46682 527 | 80.5 48.269861 528 | 81.5 14.059131 529 | 82.5 33.059344 530 | 83.5 21.259768 531 | 84.5 -10.769794 532 | 85.5 -18.832321 533 | 86.5 -36.303653 534 | 87.5 -29.189988 535 | 88.5 -34.868463 536 | 89.5 -41.195371 537 | 90.5 -54.969137 538 | 91.5 -26.579642 539 | 92.5 -16.649134 540 | 93.5 -8.9529273 541 | 94.5 7.3638513 542 | 95.5 -33.581095 543 | & 544 | 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73 301.1073 372 | 74 299.88596 373 | 75 297.85382 374 | 76 298.68292 375 | 77 300.73163 376 | 78 302.16425 377 | 79 301.41513 378 | 80 299.98892 379 | 81 296.83643 380 | 82 300.56674 381 | 83 298.62955 382 | 84 298.46661 383 | 85 299.11243 384 | 86 301.20126 385 | 87 299.59982 386 | 88 299.5098 387 | 89 301.62509 388 | 90 300.24704 389 | 91 300.05057 390 | 92 298.42136 391 | 93 299.73923 392 | 94 301.10901 393 | 95 300.15652 394 | 96 301.76077 395 | 97 299.34586 396 | 98 302.36755 397 | 99 300.78046 398 | 100 299.06726 399 | & 400 | -------------------------------------------------------------------------------- /figures/plot_lyso_nvt_temperature.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/figures/plot_lyso_nvt_temperature.png -------------------------------------------------------------------------------- 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Living Journal of Computational Molecular Sciences ([LiveCoMS](http://www.livecomsjournal.org/)) using GitHub 2 | 3 | ## LaTeX and GitHub 4 | 5 | LaTeX is a powerful typesetting program that is very commonly used in the mathematics and physics community, and increasingly in the computational sciences. 6 | We have provided a LaTeX template for use with LiveCoMS articles in order to make it easy to have a pleasing, consistent visual style. 7 | 8 | We request that articles developed for LiveCoMS do so by creating a GitHub repository for the paper. 9 | GitHub was created to be able to easily manage code versioning, merging, and branching for software development. 10 | We feel that for collaborative documents like the ones in LiveCoMS, which encourage feedback from the community, and not just for authors, this software model is a very good fit. 11 | See a more on-depth discussion of this in [brief explanation of "paper writing as code development"](http://https://github.com/livecomsjournal/journal_information/blob/master/editorial_material/PAPER_CODE.md) for this model we are using for LiveCoMS. 12 | 13 | ### Setting up and Managing a GitHub repository 14 | 15 | GitHub has a substantial set of online tutorials and answered questions. [It is very easy to set up a repository in GitHub](https://help.github.com/articles/create-a-repo/). 16 | 17 | Some particular recommendations we have when you set up your GitHub repository. 18 | - Use the issue tracker. The [issue tracker model](https://guides.github.com/features/issues/) is a powerful way to manage contributions from a number of different authors and contributors, and allow community engagement with your work. 19 | - [Protect the master branch](https://help.github.com/articles/about-protected-branches/); if people are changing the master branch directly, it will be much harder to track revisions and make sure changes are edited before being incorporated. 20 | - We recommend adding changes to the repository [through pull requests](https://help.github.com/articles/proposing-changes-to-your-work-with-pull-requests/). In this way, other people can easily see what changes are being requested and made. Pull requests can be made from a branch of your repository (if from one of your co-authors) or from a fork of your repository (if from an outside individual who would like to contribute) and are handled similarly in either case -- the repository owners review and decide whether or not to acccept the proposed changes. 21 | 22 | ### Versioning and dates 23 | 24 | All versions of your article should be dated; our templates automatically add a date to each compilation of the PDF, and when you make changes to your content, you should include an updated version of the PDF in your repository. 25 | 26 | **Versioning of articles occurs via two mechanisms which should work together**: 27 | - LiveCoMS templates use titles which have a version number explicitly stated in the title. Change this version whenever you make a significant change, using a numbering scheme you agree on with your co-authors and, ideally, document here. 28 | - GitHub has a mechanism to archive specific versions of code (in this case, your paper!) as specific "releases". Whenever you increment the version number in your title, you should also [create a new release on GitHub](https://help.github.com/articles/creating-releases/) to archive it and concisely describe any associated changes. 29 | 30 | It is also possible to easily set up tools like Zenodo to automatically generate a new DOI for each release of a project, if you so desire. 31 | 32 | #### Versioning and LiveCoMS 33 | 34 | Please note that versioning on GitHub is your choice and is separate from the process of publishing new peer-reviewed versions in LiveCoMS. 35 | Each version you publish in LiveCoMS must have a unique version number, but these version numbers are up to you, and can track with what is used on your GitHub repository. 36 | For example, you might choose to give your first published version on LiveCoMS the version number 1.0, but if in two years it makes sense to do a new peer-reviewed version, this could hypothetically be version 2.4, if that's what your GitHub repository is at. 37 | 38 | #### Change logs 39 | 40 | We recommend you keep track of even minor changes in a running log near the bottom of the base `README.md` file in your repository, and any time enough minor changes accumulate, create a new version number and release to clearly indicate that these have been incorporated and update your revision log. 41 | This will allow readers to easily track progress of your document over time without having to navigate the full commit history on GitHub. 42 | 43 | #### Example scenarios for authors 44 | 45 | Perhaps you've just come out with a new Best Practices article for LiveCoMS, and several community members are very interested and contact you via your issue tracker with ideas for other material which could be included, and another contacts you by e-mail. 46 | We strongly recommend funneling as much discusion as possible to your GitHub issue tracker since it will allow interested individuals to discuss publicly and openly, which e-mail does not. 47 | So, first, we suggest referring the e-mail contact to GitHub (if he or she is interested). 48 | For individuals who suggest including new material, if you are receptive, you have several options: 49 | - Write material like what they suggest and incorporate it (acknowledging them as appropriate) 50 | - See if they are interested in actually providing draft material for you to incorporate; this could come in as a pull request (where they request to change your document and you review and propose modifications and accept it if you're happy with it) or they could just provide you with content. The former is preferable since GitHub will then formally track their contribution. One issue to consider in this case is whether their contributions will merit addition as an author. You should work this out with them before they provide significant draft content. Note that you CAN add authors to your document, though authorship will not change at LiveCoMS until a new peer reviewed version is published. 51 | 52 | In either case you would close the relevant GitHub issue once addressed. 53 | 54 | #### Example scenarios for readers 55 | 56 | Perhaps you've just found a LiveCoMS article which interests you greatly, and you see some important references it missed or have an idea for other material which really ought to be included. 57 | We recommend that your first step be to raise an issue on the repository's issue tracker, discussing your observations and asking the authors' opinion about how to handle it. 58 | You should be sure to indicate the nature of your interest. 59 | For example, you might say: 60 | - I just wanted to make sure you were aware of this in case you would like to discuss it 61 | - I believe you should write new content which discusses and/or cites this for the following reasons 62 | - I'm very interested in this work and would be happy to contribute to it by adding material along these lines if you are interested, or if not, I could give you some suggestions on relevant references if you would like to investigate 63 | 64 | Basically, try to give authors some sense of how interested you are, how strongly you feel about the issue, and whether you are willing to get involved or just providing feedback. 65 | Be aware that some authors may be delighted to add new authors and contributions to a paper, whereas others may want to keep the authors list short and tightly curate everything. 66 | DO make sure that, if you head towards actually writing any content for inclusion, everyone's expectations about authorship are clear in advance. 67 | 68 | If you do end up writing something, you will likely need to make a fork of the repository, make your changes on that fork, and then submit a pull request from your fork in order to change the repository. 69 | If you head this route, be sure you have read the [LiveCoMS authors guide](https://livecomsjournal.github.io/authors/), as you want to make sure your changes continue to conform to what LiveCoMS requires. 70 | 71 | ### Some LaTeX formatting tips 72 | 73 | - Keep your paper in one sentence per line. This makes it easy to see which sentences have changed when you look at the diff between one version and the next. The GitHub diff tools operate on a per-line basis. If there are no line breaks between sentences, then other authors will see only that something somewhere in the paragraph has changed. 74 | -------------------------------------------------------------------------------- /releases/LiveCoMS_Article_ASAP_V1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/releases/LiveCoMS_Article_ASAP_V1.pdf -------------------------------------------------------------------------------- /releases/LiveCoMS_Article_V1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/releases/LiveCoMS_Article_V1.pdf -------------------------------------------------------------------------------- /releases/header_V1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/releases/header_V1.png -------------------------------------------------------------------------------- /tutorial-files/README: -------------------------------------------------------------------------------- 1 | 2 | Provided here is a single archive of all input files needed to run the seven tutorials. 3 | 4 | Exact commands that are to be issued by the user are provided in the tutorial article 5 | and are also available within each tutorial at http://www.mdtutorials.com/gmx/index.html. 6 | -------------------------------------------------------------------------------- /tutorial-files/biphasic/chx.gro: -------------------------------------------------------------------------------- 1 | PRODRG COORDS 2 | 6 3 | 1CHX CAA 1 -0.086 0.815 -0.018 4 | 1CHX CAB 2 0.009 0.913 0.051 5 | 1CHX CAD 3 -0.066 1.039 0.094 6 | 1CHX CAF 4 -0.181 1.002 0.188 7 | 1CHX CAE 5 -0.277 0.905 0.120 8 | 1CHX CAC 6 -0.201 0.779 0.076 9 | 0.43600 0.43600 0.43600 10 | -------------------------------------------------------------------------------- /tutorial-files/biphasic/chx.top: -------------------------------------------------------------------------------- 1 | ; 2 | ; 3 | ; This file was generated by PRODRG version AA081006.0504 4 | ; PRODRG written/copyrighted by Daan van Aalten 5 | ; and Alexander Schuettelkopf 6 | ; 7 | ; Questions/comments to dava@davapc1.bioch.dundee.ac.uk 8 | ; 9 | ; When using this software in a publication, cite: 10 | ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). 11 | ; PRODRG - a tool for high-throughput crystallography 12 | ; of protein-ligand complexes. 13 | ; Acta Crystallogr. D60, 1355--1363. 14 | ; 15 | ; 16 | 17 | #include "gromos43a1.ff/forcefield.itp" 18 | 19 | [ moleculetype ] 20 | ; Name nrexcl 21 | CHX 3 22 | 23 | [ atoms ] 24 | ; nr type resnr resid atom cgnr charge mass 25 | 1 CH2 1 CHX CAA 1 0.000 14.0270 26 | 2 CH2 1 CHX CAB 2 0.000 14.0270 27 | 3 CH2 1 CHX CAD 3 0.000 14.0270 28 | 4 CH2 1 CHX CAF 4 0.000 14.0270 29 | 5 CH2 1 CHX CAE 5 0.000 14.0270 30 | 6 CH2 1 CHX CAC 6 0.000 14.0270 31 | 32 | [ bonds ] 33 | ; ai aj fu c0, c1, ... 34 | 1 2 2 0.152 5430000.0 0.152 5430000.0 ; CAA CAB 35 | 1 6 2 0.152 5430000.0 0.152 5430000.0 ; CAA CAC 36 | 2 3 2 0.152 5430000.0 0.152 5430000.0 ; CAB CAD 37 | 3 4 2 0.152 5430000.0 0.152 5430000.0 ; CAD CAF 38 | 4 5 2 0.152 5430000.0 0.152 5430000.0 ; CAF CAE 39 | 5 6 2 0.152 5430000.0 0.152 5430000.0 ; CAE CAC 40 | 41 | [ pairs ] 42 | ; ai aj fu c0, c1, ... 43 | 1 4 1 ; CAA CAF 44 | 2 5 1 ; CAB CAE 45 | 3 6 1 ; CAD CAC 46 | 47 | [ angles ] 48 | ; ai aj ak fu c0, c1, ... 49 | 2 1 6 2 109.5 520.0 109.5 520.0 ; CAB CAA CAC 50 | 1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB CAD 51 | 2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAD CAF 52 | 3 4 5 2 109.5 520.0 109.5 520.0 ; CAD CAF CAE 53 | 4 5 6 2 109.5 520.0 109.5 520.0 ; CAF CAE CAC 54 | 1 6 5 2 109.5 520.0 109.5 520.0 ; CAA CAC CAE 55 | 56 | [ dihedrals ] 57 | ; ai aj ak al fu c0, c1, m, ... 58 | 3 2 1 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAB CAA CAC 59 | 5 6 1 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAC CAA CAB 60 | 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAD CAB CAA 61 | 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAF CAD CAB 62 | 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAC CAE CAF CAD 63 | 1 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAC CAE CAF 64 | 65 | ; include water 66 | #include "spc.itp" 67 | 68 | [ system ] 69 | Cyclohexane box 70 | 71 | [ molecules ] 72 | CHX 466 73 | -------------------------------------------------------------------------------- /tutorial-files/complex/em.mdp: -------------------------------------------------------------------------------- 1 | ; LINES STARTING WITH ';' ARE COMMENTS 2 | title = Minimization ; Title of run 3 | 4 | ; Parameters describing what to do, when to stop and what to save 5 | integrator = steep ; Algorithm (steep = steepest descent minimization) 6 | emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol 7 | emstep = 0.01 ; Energy step size 8 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 9 | 10 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 11 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 12 | cutoff-scheme = Verlet 13 | ns_type = grid ; Method to determine neighbor list (simple, grid) 14 | rlist = 1.2 ; Cut-off for making neighbor list (short range forces) 15 | coulombtype = PME ; Treatment of long range electrostatic interactions 16 | rcoulomb = 1.2 ; long range electrostatic cut-off 17 | vdwtype = cutoff 18 | vdw-modifier = force-switch 19 | rvdw-switch = 1.0 20 | rvdw = 1.2 ; long range Van der Waals cut-off 21 | pbc = xyz ; Periodic Boundary Conditions 22 | DispCorr = no 23 | -------------------------------------------------------------------------------- /tutorial-files/complex/gromos54a7_atb.ff.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/tutorial-files/complex/gromos54a7_atb.ff.tar.gz -------------------------------------------------------------------------------- /tutorial-files/complex/ions.mdp: -------------------------------------------------------------------------------- 1 | ; LINES STARTING WITH ';' ARE COMMENTS 2 | title = Minimization ; Title of run 3 | 4 | ; Parameters describing what to do, when to stop and what to save 5 | integrator = steep ; Algorithm (steep = steepest descent minimization) 6 | emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol 7 | emstep = 0.01 ; Energy step size 8 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 9 | 10 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 11 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 12 | cutoff-scheme = Verlet 13 | ns_type = grid ; Method to determine neighbor list (simple, grid) 14 | rlist = 1.0 ; Cut-off for making neighbor list (short range forces) 15 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 16 | rcoulomb = 1.0 ; long range electrostatic cut-off 17 | rvdw = 1.0 ; long range Van der Waals cut-off 18 | pbc = xyz ; Periodic Boundary Conditions 19 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | JZ4 3 | 22 22 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C4 24.2940 -24.1240 -0.0710 C.3 1 JZ4 -0.0650 9 | 2 C7 21.5530 -27.2140 -4.1120 C.ar 1 JZ4 -0.0613 10 | 3 C8 22.0680 -26.7470 -5.3310 C.ar 1 JZ4 -0.0583 11 | 4 C9 22.6710 -25.5120 -5.4480 C.ar 1 JZ4 -0.0199 12 | 5 C10 22.7690 -24.7300 -4.2950 C.ar 1 JZ4 0.1200 13 | 6 C11 21.6930 -26.4590 -2.9540 C.ar 1 JZ4 -0.0551 14 | 7 C12 22.2940 -25.1870 -3.0750 C.ar 1 JZ4 -0.0060 15 | 8 C13 22.4630 -24.4140 -1.8080 C.3 1 JZ4 -0.0245 16 | 9 C14 23.9250 -24.7040 -1.3940 C.3 1 JZ4 -0.0518 17 | 10 OAB 23.4120 -23.5360 -4.3420 O.3 1 JZ4 -0.5065 18 | 11 H 25.3133 -24.3619 0.1509 H 1 JZ4 0.0230 19 | 12 H 23.6591 -24.5327 0.6872 H 1 JZ4 0.0230 20 | 13 H 24.1744 -23.0611 -0.1016 H 1 JZ4 0.0230 21 | 14 H 21.0673 -28.1238 -4.0754 H 1 JZ4 0.0618 22 | 15 H 21.9931 -27.3472 -6.1672 H 1 JZ4 0.0619 23 | 16 H 23.0361 -25.1783 -6.3537 H 1 JZ4 0.0654 24 | 17 H 21.3701 -26.8143 -2.0405 H 1 JZ4 0.0621 25 | 18 H 21.7794 -24.7551 -1.0588 H 1 JZ4 0.0314 26 | 19 H 22.2659 -23.3694 -1.9301 H 1 JZ4 0.0314 27 | 20 H 24.5755 -24.2929 -2.1375 H 1 JZ4 0.0266 28 | 21 H 24.0241 -25.7662 -1.3110 H 1 JZ4 0.0266 29 | 22 H 23.7394 -23.2120 -5.1580 H 1 JZ4 0.2921 30 | @BOND 31 | 1 4 3 ar 32 | 2 4 5 ar 33 | 3 3 2 ar 34 | 4 10 5 1 35 | 5 5 7 ar 36 | 6 2 6 ar 37 | 7 7 6 ar 38 | 8 7 8 1 39 | 9 8 9 1 40 | 10 9 1 1 41 | 11 1 11 1 42 | 12 1 12 1 43 | 13 1 13 1 44 | 14 2 14 1 45 | 15 3 15 1 46 | 16 4 16 1 47 | 17 6 17 1 48 | 18 8 18 1 49 | 19 8 19 1 50 | 20 9 20 1 51 | 21 9 21 1 52 | 22 10 22 1 53 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4.pdb: -------------------------------------------------------------------------------- 1 | REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JZ4 A 167 2 | HET JZ4 A 167 10 3 | HETNAM JZ4 2-PROPYLPHENOL 4 | FORMUL 4 JZ4 C9 H12 O 5 | HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C 6 | HETATM 1377 C7 JZ4 A 167 21.553 -27.214 -4.112 1.00 16.92 C 7 | HETATM 1378 C8 JZ4 A 167 22.068 -26.747 -5.331 1.00 14.84 C 8 | HETATM 1379 C9 JZ4 A 167 22.671 -25.512 -5.448 1.00 15.93 C 9 | HETATM 1380 C10 JZ4 A 167 22.769 -24.730 -4.295 1.00 15.43 C 10 | HETATM 1381 C11 JZ4 A 167 21.693 -26.459 -2.954 1.00 16.72 C 11 | HETATM 1382 C12 JZ4 A 167 22.294 -25.187 -3.075 1.00 14.13 C 12 | HETATM 1383 C13 JZ4 A 167 22.463 -24.414 -1.808 1.00 15.94 C 13 | HETATM 1384 C14 JZ4 A 167 23.925 -24.704 -1.394 1.00 15.28 C 14 | HETATM 1385 OAB JZ4 A 167 23.412 -23.536 -4.342 1.00 13.88 O 15 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4.str: -------------------------------------------------------------------------------- 1 | * Toppar stream file generated by 2 | * CHARMM General Force Field (CGenFF) program version 1.0.0 3 | * For use with CGenFF version 3.0.1 4 | * 5 | 6 | read rtf card append 7 | * Topologies generated by 8 | * CHARMM General Force Field (CGenFF) program version 1.0.0 9 | * 10 | 36 1 11 | 12 | ! "penalty" is the highest penalty score of the associated parameters. 13 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 14 | ! and 50 mean some basic validation is recommended; penalties higher than 15 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 16 | 17 | RESI JZ4 0.000 ! param penalty= 0.900 ; charge penalty= 0.342 18 | GROUP ! CHARGE CH_PENALTY 19 | ATOM C1 CG331 -0.271 ! 0.285 20 | ATOM C2 CG321 -0.183 ! 0.045 21 | ATOM C3 CG321 -0.178 ! 0.342 22 | ATOM C4 CG2R61 -0.007 ! 0.218 23 | ATOM C9 CG2R61 0.103 ! 0.030 24 | ATOM O10 OG311 -0.529 ! 0.190 25 | ATOM H22 HGP1 0.420 ! 0.000 26 | ATOM C8 CG2R61 -0.110 ! 0.000 27 | ATOM H21 HGR61 0.115 ! 0.000 28 | ATOM C5 CG2R61 -0.115 ! 0.000 29 | ATOM H18 HGR61 0.115 ! 0.000 30 | ATOM C6 CG2R61 -0.108 ! 0.000 31 | ATOM H19 HGR61 0.115 ! 0.000 32 | ATOM C7 CG2R61 -0.112 ! 0.000 33 | ATOM H20 HGR61 0.115 ! 0.000 34 | ATOM H1 HGA3 0.090 ! 0.000 35 | ATOM H2 HGA3 0.090 ! 0.000 36 | ATOM H3 HGA3 0.090 ! 0.000 37 | ATOM H4 HGA2 0.090 ! 0.000 38 | ATOM H5 HGA2 0.090 ! 0.000 39 | ATOM H6 HGA2 0.090 ! 0.000 40 | ATOM H7 HGA2 0.090 ! 0.000 41 | 42 | BOND C1 C2 43 | BOND C2 C3 44 | BOND C3 C4 45 | BOND C4 C9 46 | BOND C4 C5 47 | BOND C9 O10 48 | BOND C9 C8 49 | BOND O10 H22 50 | BOND C8 H21 51 | BOND C8 C7 52 | BOND C5 H18 53 | BOND C5 C6 54 | BOND C6 H19 55 | BOND C6 C7 56 | BOND C7 H20 57 | BOND C1 H1 58 | BOND C1 H2 59 | BOND C1 H3 60 | BOND C2 H4 61 | BOND C2 H5 62 | BOND C3 H6 63 | BOND C3 H7 64 | 65 | END 66 | 67 | read param card flex append 68 | * Parameters generated by analogy by 69 | * CHARMM General Force Field (CGenFF) program version 1.0.0 70 | * 71 | 72 | ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 73 | ! and 50 mean some basic validation is recommended; penalties higher than 74 | ! 50 indicate poor analogy and mandate extensive validation/optimization. 75 | 76 | BONDS 77 | 78 | ANGLES 79 | 80 | DIHEDRALS 81 | CG321 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! ***** , from CG311 CG2R61 CG2R61 OG311, penalty= 0.6 82 | CG2R61 CG321 CG321 CG331 0.0400 3 0.00 ! ***** , from CG2R61 CG321 CG321 CG321, penalty= 0.9 83 | 84 | IMPROPERS 85 | 86 | END 87 | RETURN 88 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4_UA.pdb: -------------------------------------------------------------------------------- 1 | HEADER UNCLASSIFIED 05-Jun-18 2 | TITLE UNITED ATOM STRUCTURE FOR MOLECULE UNK 3 | AUTHOR GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2018-06-04 12:59:49 4 | AUTHOR 2 http://compbio.biosci.uq.edu.au/atb 5 | HETATM 1 C1 LJ4C 0 3.743 -0.302 0.241 1.00 0.00 C 6 | HETATM 2 C2 LJ4C 0 2.255 -0.280 0.599 1.00 0.00 C 7 | HETATM 3 C3 LJ4C 0 1.421 -0.315 -0.684 1.00 0.00 C 8 | HETATM 4 C4 LJ4C 0 -0.044 -0.293 -0.331 1.00 0.00 C 9 | HETATM 5 C9 LJ4C 0 -0.684 0.916 -0.100 1.00 0.00 C 10 | HETATM 6 O10 LJ4C 0 0.007 2.082 -0.195 1.00 0.00 O 11 | HETATM 7 H22 LJ4C 0 0.410 2.370 0.635 1.00 0.00 H 12 | HETATM 8 C8 LJ4C 0 -2.034 0.933 0.220 1.00 0.00 C 13 | HETATM 9 H21 LJ4C 0 -2.536 1.872 0.396 1.00 0.00 H 14 | HETATM 10 C5 LJ4C 0 -0.749 -1.477 -0.233 1.00 0.00 C 15 | HETATM 11 H18 LJ4C 0 -0.250 -2.418 -0.409 1.00 0.00 H 16 | HETATM 12 C6 LJ4C 0 -2.093 -1.458 0.091 1.00 0.00 C 17 | HETATM 13 H19 LJ4C 0 -2.642 -2.384 0.167 1.00 0.00 H 18 | HETATM 14 C7 LJ4C 0 -2.735 -0.254 0.317 1.00 0.00 C 19 | HETATM 15 H20 LJ4C 0 -3.785 -0.242 0.570 1.00 0.00 H 20 | CONECT 1 2 21 | CONECT 2 1 3 22 | CONECT 3 2 4 23 | CONECT 4 3 5 10 24 | CONECT 5 4 6 8 25 | CONECT 6 5 7 26 | CONECT 7 6 27 | CONECT 8 5 9 14 28 | CONECT 9 8 29 | CONECT 10 4 11 12 30 | CONECT 11 10 31 | CONECT 12 10 13 14 32 | CONECT 13 12 33 | CONECT 14 8 12 15 34 | CONECT 15 14 35 | END 36 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4_UA_gromos54a7.itp: -------------------------------------------------------------------------------- 1 | ;----------------------------TITLE ----------------------------------------------------------------------------------------- 2 | ; 2-Propylphenol 3 | ; 4 | ; This file was generated at 20:11 on 2018-06-05 by 5 | ; 6 | ; Automatic Topology Builder 7 | ; 8 | ; REVISION 2018-06-04 12:59:49 9 | ;--------------------------------------------------------------------------------------------------------------------------- 10 | ; Authors : Alpeshkumar K. Malde, Le Zuo, Matthew Breeze, Martin Stroet, Alan E. Mark 11 | ; 12 | ; Institute : Molecular Dynamics group, 13 | ; School of Chemistry and Molecular Biosciences (SCMB), 14 | ; The University of Queensland, QLD 4072, Australia 15 | ; URL : http://compbio.biosci.uq.edu.au/atb 16 | ; Citation : Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. 17 | ; An Automated force field Topology Builder (ATB) and repository: version 1.0. 18 | ; Journal of Chemical Theory and Computation, 2011, 7(12), 4026-4037. 19 | ; http://pubs.acs.org/doi/abs/10.1021/ct200196m 20 | ; 21 | ; Disclaimer : 22 | ; While every effort has been made to ensure the accuracy and validity of parameters provided below 23 | ; the assignment of parameters is being based on an automated procedure combining data provided by a 24 | ; given user as well as calculations performed using third party software. They are provided as a guide. 25 | ; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided 26 | ; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion 27 | ; and to perform additional validation tests for their specific application if required. Neither the authors 28 | ; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. 29 | ; 30 | ; Release notes and warnings: 31 | ; (1) The topology is based on a set of atomic coordinates and other data provided by the user after 32 | ; after quantum mechanical optimization of the structure using different levels of theory depending on 33 | ; the nature of the molecule. 34 | ; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. 35 | ; In these cases alternative type codes are provided at the end of the line. 36 | ; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral 37 | ; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" 38 | ; or "uncertain" in comments. 39 | ; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder 40 | ; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually 41 | ; before the file can be used. 42 | ;--------------------------------------------------------------------------------------------------------------------------- 43 | ; Input Structure : LJ4C 44 | ; Output : UNITED ATOM topology 45 | ; Use in conjunction with the corresponding united atom PDB file. 46 | ;--------------------------------------------------------------------------------------------------------------------------- 47 | ; Citing this topology file 48 | ; ATB molid: 36583 49 | ; ATB Topology Hash: a168b 50 | ;--------------------------------------------------------------------------------------------------------------------------- 51 | ; Final Topology Generation was performed using: 52 | ; A B3LYP/6-31G* optimized geometry. 53 | ; Bonded and van der Waals parameters were taken from the GROMOS {0} parameter set. 54 | ; Initial charges were estimated using the ESP method of Merz-Kollman. 55 | ; Final charges and charge groups were generated by method described in the ATB paper. 56 | ; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. 57 | ;--------------------------------------------------------------------------------------------------------------------------- 58 | ; 59 | ; 60 | [ moleculetype ] 61 | ; Name nrexcl 62 | LJ4C 3 63 | [ atoms ] 64 | ; nr type resnr resid atom cgnr charge mass total_charge 65 | 1 CH3 1 LJ4C C1 1 -0.085 15.0350 66 | 2 CH2 1 LJ4C C2 1 0.143 14.0270 67 | 3 CH2 1 LJ4C C3 1 0.023 14.0270 ; 0.081 68 | 4 C 1 LJ4C C4 2 -0.143 12.0110 69 | 5 C 1 LJ4C C9 2 0.341 12.0110 70 | 6 OA 1 LJ4C O10 2 -0.606 15.9994 71 | 7 HS14 1 LJ4C H22 2 0.436 1.0080 72 | 8 C 1 LJ4C C8 2 -0.284 12.0110 73 | 9 HC 1 LJ4C H21 2 0.175 1.0080 ; -0.081 74 | 10 C 1 LJ4C C5 3 -0.132 12.0110 75 | 11 HC 1 LJ4C H18 3 0.132 1.0080 ; 0.000 76 | 12 C 1 LJ4C C6 4 -0.202 12.0110 77 | 13 HC 1 LJ4C H19 4 0.170 1.0080 78 | 14 C 1 LJ4C C7 4 -0.101 12.0110 79 | 15 HC 1 LJ4C H20 4 0.133 1.0080 ; 0.000 80 | ; total charge of the molecule: 0.000 81 | [ bonds ] 82 | ; ai aj funct c0 c1 83 | 1 2 2 0.1530 7.1500e+06 84 | 2 3 2 0.1540 4.0057e+06 85 | 3 4 2 0.1520 5.4300e+06 86 | 4 5 2 0.1400 8.5400e+06 87 | 4 10 2 0.1400 8.5400e+06 88 | 5 6 2 0.1380 1.1000e+07 89 | 5 8 2 0.1390 8.6600e+06 90 | 6 7 2 0.0972 1.9581e+07 91 | 8 9 2 0.1090 1.2300e+07 92 | 8 14 2 0.1390 8.6600e+06 93 | 10 11 2 0.1090 1.2300e+07 94 | 10 12 2 0.1390 8.6600e+06 95 | 12 13 2 0.1090 1.2300e+07 96 | 12 14 2 0.1390 8.6600e+06 97 | 14 15 2 0.1090 1.2300e+07 98 | [ pairs ] 99 | ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 100 | 1 4 1 101 | 2 5 1 102 | 2 10 1 103 | 3 6 1 104 | 3 8 1 105 | 3 11 1 106 | 3 12 1 107 | 4 7 1 108 | 4 9 1 109 | 4 13 1 110 | 10 15 1 111 | 8 13 1 112 | 5 11 1 113 | 5 15 1 114 | 6 9 1 115 | 6 10 1 116 | 6 14 1 117 | 11 13 1 118 | 11 14 1 119 | 13 15 1 120 | 9 12 1 121 | 9 15 1 122 | 7 8 1 123 | [ angles ] 124 | ; ai aj ak funct angle fc 125 | 1 2 3 2 111.00 530.00 126 | 2 3 4 2 111.00 530.00 127 | 3 4 5 2 120.00 560.00 128 | 3 4 10 2 120.00 560.00 129 | 5 4 10 2 120.00 560.00 130 | 4 5 6 2 121.00 685.00 131 | 4 5 8 2 120.00 560.00 132 | 6 5 8 2 117.00 635.00 133 | 5 6 7 2 109.50 450.00 134 | 5 8 9 2 120.00 505.00 135 | 5 8 14 2 120.00 560.00 136 | 9 8 14 2 120.00 505.00 137 | 4 10 11 2 120.00 505.00 138 | 4 10 12 2 120.00 560.00 139 | 11 10 12 2 120.00 505.00 140 | 10 12 13 2 120.00 505.00 141 | 10 12 14 2 120.00 560.00 142 | 13 12 14 2 120.00 505.00 143 | 8 14 12 2 120.00 560.00 144 | 8 14 15 2 120.00 505.00 145 | 12 14 15 2 120.00 505.00 146 | [ dihedrals ] 147 | ; GROMOS improper dihedrals 148 | ; ai aj ak al funct angle fc 149 | 4 3 10 5 2 0.00 167.36 150 | 10 4 12 11 2 0.00 167.36 151 | 12 10 14 13 2 0.00 167.36 152 | 14 12 8 15 2 0.00 167.36 153 | 8 14 5 9 2 0.00 167.36 154 | 5 4 8 6 2 0.00 167.36 155 | [ dihedrals ] 156 | ; ai aj ak al funct ph0 cp mult 157 | 1 2 3 4 1 0.00 5.92 3 158 | 2 3 4 10 1 0.00 1.00 6 159 | 10 4 5 8 1 180.00 41.80 2 160 | 5 4 10 12 1 180.00 41.80 2 161 | 4 5 6 7 1 180.00 16.70 2 162 | 4 5 8 14 1 180.00 41.80 2 163 | 5 8 14 12 1 180.00 41.80 2 164 | 4 10 12 14 1 180.00 41.80 2 165 | 10 12 14 8 1 180.00 41.80 2 166 | [ exclusions ] 167 | ; ai aj funct ; GROMOS 1-4 exclusions 168 | 4 14 169 | 8 10 170 | 5 12 171 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4_allH.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | JZ4 3 | 22 22 0 0 0 4 | SMALL 5 | GASTEIGER 6 | 7 | @ATOM 8 | 1 C1 3.7430 -0.3020 0.2410 C.3 1 JZ4 -0.0650 9 | 2 C2 2.2550 -0.2800 0.5990 C.3 1 JZ4 -0.0518 10 | 3 C3 1.4210 -0.3150 -0.6840 C.3 1 JZ4 -0.0245 11 | 4 C4 -0.0440 -0.2930 -0.3310 C.ar 1 JZ4 -0.0060 12 | 5 C9 -0.6840 0.9160 -0.1000 C.ar 1 JZ4 0.1200 13 | 6 O10 0.0070 2.0820 -0.1950 O.3 1 JZ4 -0.5065 14 | 7 H22 0.4100 2.3700 0.6350 H 1 JZ4 0.2921 15 | 8 C8 -2.0340 0.9330 0.2200 C.ar 1 JZ4 -0.0199 16 | 9 H21 -2.5360 1.8720 0.3960 H 1 JZ4 0.0654 17 | 10 C5 -0.7490 -1.4770 -0.2330 C.ar 1 JZ4 -0.0551 18 | 11 H18 -0.2500 -2.4180 -0.4090 H 1 JZ4 0.0621 19 | 12 C6 -2.0930 -1.4580 0.0910 C.ar 1 JZ4 -0.0613 20 | 13 H19 -2.6420 -2.3840 0.1670 H 1 JZ4 0.0618 21 | 14 C7 -2.7350 -0.2540 0.3170 C.ar 1 JZ4 -0.0583 22 | 15 H20 -3.7850 -0.2420 0.5700 H 1 JZ4 0.0619 23 | 16 H 4.3260 -0.2775 1.1379 H 1 JZ4 0.0230 24 | 17 H 3.9778 0.5513 -0.3604 H 1 JZ4 0.0230 25 | 18 H 3.9654 -1.1951 -0.3047 H 1 JZ4 0.0230 26 | 19 H 2.0326 0.6131 1.1447 H 1 JZ4 0.0266 27 | 20 H 2.0202 -1.1333 1.2004 H 1 JZ4 0.0266 28 | 21 H 1.6431 -1.2082 -1.2296 H 1 JZ4 0.0314 29 | 22 H 1.6559 0.5380 -1.2858 H 1 JZ4 0.0314 30 | @BOND 31 | 1 1 2 1 32 | 2 2 3 1 33 | 3 3 4 1 34 | 4 4 5 ar 35 | 5 4 10 ar 36 | 6 5 6 1 37 | 7 5 8 ar 38 | 8 6 7 1 39 | 9 8 9 1 40 | 10 8 14 ar 41 | 11 10 11 1 42 | 12 10 12 ar 43 | 13 12 13 1 44 | 14 12 14 ar 45 | 15 14 15 1 46 | 16 1 16 1 47 | 17 1 17 1 48 | 18 1 18 1 49 | 19 2 19 1 50 | 20 2 20 1 51 | 21 3 21 1 52 | 22 3 22 1 53 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4_allH.pdb: -------------------------------------------------------------------------------- 1 | REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JZ4 A 167 2 | HET JZ4 A 167 10 3 | HETNAM JZ4 2-PROPYLPHENOL 4 | FORMUL 4 JZ4 C9 H12 O 5 | COMPND UNNAMED 6 | AUTHOR GENERATED BY OPEN BABEL 2.3.90 7 | ATOM 1 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 0.00 C 8 | ATOM 2 C7 JZ4 A 167 21.553 -27.214 -4.112 1.00 0.00 C 9 | ATOM 3 C8 JZ4 A 167 22.068 -26.747 -5.331 1.00 0.00 C 10 | ATOM 4 C9 JZ4 A 167 22.671 -25.512 -5.448 1.00 0.00 C 11 | ATOM 5 C10 JZ4 A 167 22.769 -24.730 -4.295 1.00 0.00 C 12 | ATOM 6 C11 JZ4 A 167 21.693 -26.459 -2.954 1.00 0.00 C 13 | ATOM 7 C12 JZ4 A 167 22.294 -25.187 -3.075 1.00 0.00 C 14 | ATOM 8 C13 JZ4 A 167 22.463 -24.414 -1.808 1.00 0.00 C 15 | ATOM 9 C14 JZ4 A 167 23.925 -24.704 -1.394 1.00 0.00 C 16 | ATOM 10 OAB JZ4 A 167 23.412 -23.536 -4.342 1.00 0.00 O 17 | HETATM 11 H UNL 1 25.313 -24.362 0.151 1.00 0.00 H 18 | HETATM 12 H UNL 1 23.659 -24.533 0.687 1.00 0.00 H 19 | HETATM 13 H UNL 1 24.174 -23.061 -0.102 1.00 0.00 H 20 | HETATM 14 H UNL 1 21.067 -28.124 -4.075 1.00 0.00 H 21 | HETATM 15 H UNL 1 21.993 -27.347 -6.167 1.00 0.00 H 22 | HETATM 16 H UNL 1 23.036 -25.178 -6.354 1.00 0.00 H 23 | HETATM 17 H UNL 1 21.370 -26.814 -2.040 1.00 0.00 H 24 | HETATM 18 H UNL 1 21.779 -24.755 -1.059 1.00 0.00 H 25 | HETATM 19 H UNL 1 22.266 -23.369 -1.930 1.00 0.00 H 26 | HETATM 20 H UNL 1 24.576 -24.293 -2.137 1.00 0.00 H 27 | HETATM 21 H UNL 1 24.024 -25.766 -1.311 1.00 0.00 H 28 | HETATM 22 H UNL 1 23.739 -23.212 -5.158 1.00 0.00 H 29 | CONECT 1 9 11 12 13 30 | CONECT 2 3 6 14 31 | CONECT 3 4 2 15 32 | CONECT 4 3 5 16 33 | CONECT 5 4 10 7 34 | CONECT 6 2 7 17 35 | CONECT 7 5 6 8 36 | CONECT 8 7 9 18 19 37 | CONECT 9 8 1 20 21 38 | CONECT 10 5 22 39 | CONECT 11 1 40 | CONECT 12 1 41 | CONECT 13 1 42 | CONECT 14 2 43 | CONECT 15 3 44 | CONECT 16 4 45 | CONECT 17 6 46 | CONECT 18 8 47 | CONECT 19 8 48 | CONECT 20 9 49 | CONECT 21 9 50 | CONECT 22 10 51 | MASTER 0 0 0 0 0 0 0 0 22 0 22 0 52 | END 53 | -------------------------------------------------------------------------------- /tutorial-files/complex/jz4_ini.pdb: -------------------------------------------------------------------------------- 1 | ATOM 1 C1 JZ4 1 24.294 -24.124 -0.071 1.00 0.00 2 | ATOM 2 C2 JZ4 1 21.553 -27.214 -4.112 1.00 0.00 3 | ATOM 3 C3 JZ4 1 22.068 -26.747 -5.331 1.00 0.00 4 | ATOM 4 C4 JZ4 1 22.671 -25.512 -5.448 1.00 0.00 5 | ATOM 5 C9 JZ4 1 22.769 -24.730 -4.295 1.00 0.00 6 | ATOM 6 O10 JZ4 1 21.693 -26.459 -2.954 1.00 0.00 7 | ATOM 7 H22 JZ4 1 22.294 -25.187 -3.075 1.00 0.00 8 | ATOM 8 C8 JZ4 1 22.463 -24.414 -1.808 1.00 0.00 9 | ATOM 9 H21 JZ4 1 23.925 -24.704 -1.394 1.00 0.00 10 | ATOM 10 C5 JZ4 1 23.412 -23.536 -4.342 1.00 0.00 11 | ATOM 11 H18 JZ4 1 25.313 -24.362 0.151 1.00 0.00 12 | ATOM 12 C6 JZ4 1 23.659 -24.533 0.687 1.00 0.00 13 | ATOM 13 H19 JZ4 1 24.174 -23.061 -0.102 1.00 0.00 14 | ATOM 14 C7 JZ4 1 21.067 -28.124 -4.075 1.00 0.00 15 | ATOM 15 H20 JZ4 1 21.993 -27.347 -6.167 1.00 0.00 16 | ATOM 16 H1 JZ4 1 23.036 -25.178 -6.354 1.00 0.00 17 | ATOM 17 H2 JZ4 1 21.370 -26.814 -2.041 1.00 0.00 18 | ATOM 18 H3 JZ4 1 21.779 -24.755 -1.059 1.00 0.00 19 | ATOM 19 H4 JZ4 1 22.266 -23.369 -1.930 1.00 0.00 20 | ATOM 20 H5 JZ4 1 24.576 -24.293 -2.138 1.00 0.00 21 | ATOM 21 H6 JZ4 1 24.024 -25.766 -1.311 1.00 0.00 22 | ATOM 22 H7 JZ4 1 23.739 -23.212 -5.158 1.00 0.00 23 | END 24 | -------------------------------------------------------------------------------- /tutorial-files/complex/md.mdp: -------------------------------------------------------------------------------- 1 | title = Protein-ligand complex MD simulation 2 | ; Run parameters 3 | integrator = md ; leap-frog integrator 4 | nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns) 5 | dt = 0.002 ; 2 fs 6 | ; Output control 7 | nstenergy = 5000 ; save energies every 10.0 ps 8 | nstlog = 5000 ; update log file every 10.0 ps 9 | nstxout-compressed = 5000 ; save coordinates every 10.0 ps 10 | ; Bond parameters 11 | continuation = yes ; continuing from NPT 12 | constraint_algorithm = lincs ; holonomic constraints 13 | constraints = h-bonds ; bonds to H are constrained 14 | lincs_iter = 1 ; accuracy of LINCS 15 | lincs_order = 4 ; also related to accuracy 16 | ; Neighbor searching and vdW 17 | cutoff-scheme = Verlet 18 | ns_type = grid ; search neighboring grid cells 19 | nstlist = 20 ; largely irrelevant with Verlet 20 | rlist = 1.2 21 | vdwtype = cutoff 22 | vdw-modifier = force-switch 23 | rvdw-switch = 1.0 24 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 25 | ; Electrostatics 26 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 27 | rcoulomb = 1.2 28 | pme_order = 4 ; cubic interpolation 29 | fourierspacing = 0.16 ; grid spacing for FFT 30 | ; Temperature coupling 31 | tcoupl = V-rescale ; modified Berendsen thermostat 32 | tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate 33 | tau_t = 0.1 0.1 ; time constant, in ps 34 | ref_t = 300 300 ; reference temperature, one for each group, in K 35 | ; Pressure coupling 36 | pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT 37 | pcoupltype = isotropic ; uniform scaling of box vectors 38 | tau_p = 2.0 ; time constant, in ps 39 | ref_p = 1.0 ; reference pressure, in bar 40 | compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 41 | ; Periodic boundary conditions 42 | pbc = xyz ; 3-D PBC 43 | ; Dispersion correction is not used for proteins with the C36 additive FF 44 | DispCorr = no 45 | ; Velocity generation 46 | gen_vel = no ; continuing from NPT equilibration 47 | -------------------------------------------------------------------------------- /tutorial-files/complex/npt.mdp: -------------------------------------------------------------------------------- 1 | title = Protein-ligand complex NPT equilibration 2 | define = -DPOSRES ; position restrain the protein and ligand 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstenergy = 500 ; save energies every 1.0 ps 9 | nstlog = 500 ; update log file every 1.0 ps 10 | nstxout-compressed = 500 ; save coordinates every 1.0 ps 11 | ; Bond parameters 12 | continuation = yes ; continuing from NVT 13 | constraint_algorithm = lincs ; holonomic constraints 14 | constraints = h-bonds ; bonds to H are constrained 15 | lincs_iter = 1 ; accuracy of LINCS 16 | lincs_order = 4 ; also related to accuracy 17 | ; Neighbor searching and vdW 18 | cutoff-scheme = Verlet 19 | ns_type = grid ; search neighboring grid cells 20 | nstlist = 20 ; largely irrelevant with Verlet 21 | rlist = 1.2 22 | vdwtype = cutoff 23 | vdw-modifier = force-switch 24 | rvdw-switch = 1.0 25 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 26 | ; Electrostatics 27 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 28 | rcoulomb = 1.2 29 | pme_order = 4 ; cubic interpolation 30 | fourierspacing = 0.16 ; grid spacing for FFT 31 | ; Temperature coupling 32 | tcoupl = V-rescale ; modified Berendsen thermostat 33 | tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate 34 | tau_t = 0.1 0.1 ; time constant, in ps 35 | ref_t = 300 300 ; reference temperature, one for each group, in K 36 | ; Pressure coupling 37 | pcoupl = Berendsen ; pressure coupling is on for NPT 38 | pcoupltype = isotropic ; uniform scaling of box vectors 39 | tau_p = 2.0 ; time constant, in ps 40 | ref_p = 1.0 ; reference pressure, in bar 41 | compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 42 | refcoord_scaling = com 43 | ; Periodic boundary conditions 44 | pbc = xyz ; 3-D PBC 45 | ; Dispersion correction is not used for proteins with the C36 additive FF 46 | DispCorr = no 47 | ; Velocity generation 48 | gen_vel = no ; velocity generation off after NVT 49 | -------------------------------------------------------------------------------- /tutorial-files/complex/nvt.mdp: -------------------------------------------------------------------------------- 1 | title = Protein-ligand complex NVT equilibration 2 | define = -DPOSRES ; position restrain the protein and ligand 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstenergy = 500 ; save energies every 1.0 ps 9 | nstlog = 500 ; update log file every 1.0 ps 10 | nstxout-compressed = 500 ; save coordinates every 1.0 ps 11 | ; Bond parameters 12 | continuation = no ; first dynamics run 13 | constraint_algorithm = lincs ; holonomic constraints 14 | constraints = h-bonds ; bonds to H are constrained 15 | lincs_iter = 1 ; accuracy of LINCS 16 | lincs_order = 4 ; also related to accuracy 17 | ; Neighbor searching and vdW 18 | cutoff-scheme = Verlet 19 | ns_type = grid ; search neighboring grid cells 20 | nstlist = 20 ; largely irrelevant with Verlet 21 | rlist = 1.2 22 | vdwtype = cutoff 23 | vdw-modifier = force-switch 24 | rvdw-switch = 1.0 25 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 26 | ; Electrostatics 27 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 28 | rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) 29 | pme_order = 4 ; cubic interpolation 30 | fourierspacing = 0.16 ; grid spacing for FFT 31 | ; Temperature coupling 32 | tcoupl = V-rescale ; modified Berendsen thermostat 33 | tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate 34 | tau_t = 0.1 0.1 ; time constant, in ps 35 | ref_t = 300 300 ; reference temperature, one for each group, in K 36 | ; Pressure coupling 37 | pcoupl = no ; no pressure coupling in NVT 38 | ; Periodic boundary conditions 39 | pbc = xyz ; 3-D PBC 40 | ; Dispersion correction is not used for proteins with the C36 additive FF 41 | DispCorr = no 42 | ; Velocity generation 43 | gen_vel = yes ; assign velocities from Maxwell distribution 44 | gen_temp = 300 ; temperature for Maxwell distribution 45 | gen_seed = -1 ; generate a random seed 46 | -------------------------------------------------------------------------------- /tutorial-files/complex/sort_mol2_bonds.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | 5 | # sort_mol2_bonds.pl - a script to reorder the listing in a .mol2 @BOND 6 | # section so that the following conventions are preserved: 7 | # 1. Atoms on each line are in increasing order (e.g. 1 2 not 2 1) 8 | # 2. The bonds appear in order of ascending atom number 9 | # 3. For bonds involving the same atom in the first position, the bonds appear 10 | # in order of ascending second atom 11 | # 12 | # Written by: Justin Lemkul (jalemkul@vt.edu) 13 | # 14 | # Distributed under the GPL-3.0 license 15 | 16 | unless (scalar(@ARGV)==2) 17 | { 18 | die "Usage: perl sort_mol2_bonds.pl input.mol2 output.mol2\n"; 19 | } 20 | 21 | my $input = $ARGV[0]; 22 | my $output = $ARGV[1]; 23 | 24 | open(IN, "<$input") || die "Cannot open $input: $!\n"; 25 | my @in = ; 26 | close(IN); 27 | 28 | open(OUT, ">$output") || die "Cannot open $output: $!\n"; 29 | 30 | # get number of atoms and number of bonds from mol2 file 31 | my @tmp = split(" ", $in[2]); 32 | my $natom = $tmp[0]; 33 | my $nbond = $tmp[1]; 34 | 35 | # print out everything up until the bond section 36 | my $i=0; 37 | while (!($in[$i] =~ /BOND/)) 38 | { 39 | print OUT $in[$i]; 40 | $i++; 41 | } 42 | 43 | # print the bond section header line to output 44 | print OUT $in[$i]; 45 | $i++; 46 | 47 | # read in the bonds and sort them 48 | my $bondfmt = "%6d%6d%6d%5s\n"; 49 | my @tmparray; 50 | 51 | # sort the bonds - e.g. the one that has the 52 | # lowest atom number in the first position and then the 53 | # lowest atom number in the second position (swap if necessary) 54 | for (my $j=0; $j<$nbond; $j++) 55 | { 56 | my @tmp = split(" ", $in[$i+$j]); 57 | # parse atom numbers 58 | my $ai = $tmp[1]; 59 | my $aj = $tmp[2]; 60 | # reorder if second atom number < first 61 | if ($aj < $ai) 62 | { 63 | $ai = $tmp[2]; 64 | $aj = $tmp[1]; 65 | } 66 | # store new lines in a temporary array 67 | $tmparray[$j] = sprintf($bondfmt, $tmp[0], $ai, $aj, $tmp[3]); 68 | } 69 | 70 | # loop over tmparray to find each atom number 71 | my $nbond = 0; 72 | for (my $x=1; $x<=$natom; $x++) 73 | { 74 | my @bondarray; 75 | my $ntmp = scalar(@tmparray); 76 | for (my $b=0; $b<$ntmp; $b++) 77 | { 78 | my @tmp = split(" ", $tmparray[$b]); 79 | if ($tmp[1] == $x) 80 | { 81 | push(@bondarray, $tmparray[$b]); 82 | splice(@tmparray, $b, 1); 83 | $ntmp--; 84 | $b--; 85 | } 86 | } 87 | 88 | if (scalar(@bondarray) > 0) # some atoms will only appear in $aj, not $ai 89 | { 90 | my $nbondarray = scalar(@bondarray); 91 | if ($nbondarray > 1) 92 | { 93 | # loop over all bonds, find the one with lowest $aj 94 | # and then print it 95 | for (my $y=0; $y<$nbondarray; $y++) 96 | { 97 | my @tmp2 = split(" ", $bondarray[$y]); 98 | my $tmpatom = $tmp[2]; 99 | my $lowindex = 0; 100 | if ($tmp2[2] < $tmpatom) 101 | { 102 | $lowindex = $y; 103 | } 104 | my $keep = splice(@bondarray, $lowindex, 1); 105 | $y--; 106 | $nbondarray--; 107 | my @sorted = split(" ", $keep); 108 | $nbond++; 109 | printf OUT $bondfmt, $nbond, $sorted[1], $sorted[2], $sorted[3]; 110 | } 111 | } 112 | else 113 | { 114 | $nbond++; 115 | my @tmp2 = split(" ", $bondarray[0]); 116 | printf OUT $bondfmt, $nbond, $tmp2[1], $tmp2[2], $tmp2[3]; 117 | } 118 | } 119 | } 120 | 121 | close(OUT); 122 | 123 | exit; 124 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/em_steep.mdp: -------------------------------------------------------------------------------- 1 | ; Run control 2 | integrator = steep 3 | nsteps = 5000 4 | ; EM criteria and other stuff 5 | emtol = 100 6 | emstep = 0.01 7 | niter = 20 8 | nbfgscorr = 10 9 | ; Output control 10 | nstlog = 1 11 | nstenergy = 1 12 | ; Neighborsearching and short-range nonbonded interactions 13 | cutoff-scheme = verlet 14 | nstlist = 1 15 | ns_type = grid 16 | pbc = xyz 17 | rlist = 1.2 18 | ; Electrostatics 19 | coulombtype = PME 20 | rcoulomb = 1.2 21 | ; van der Waals 22 | vdwtype = cutoff 23 | vdw-modifier = potential-switch 24 | rvdw-switch = 1.0 25 | rvdw = 1.2 26 | ; Apply long range dispersion corrections for Energy and Pressure 27 | DispCorr = EnerPres 28 | ; Spacing for the PME/PPPM FFT grid 29 | fourierspacing = 0.12 30 | ; EWALD/PME/PPPM parameters 31 | pme_order = 6 32 | ewald_rtol = 1e-06 33 | epsilon_surface = 0 34 | ; Temperature and pressure coupling are off during EM 35 | tcoupl = no 36 | pcoupl = no 37 | ; Free energy control stuff 38 | free_energy = yes 39 | init_lambda_state = 0 40 | delta_lambda = 0 41 | calc_lambda_neighbors = 1 ; only immediate neighboring windows 42 | couple-moltype = Methane ; name of moleculetype to decouple 43 | couple-lambda0 = vdw ; only van der Waals interactions 44 | couple-lambda1 = none ; turn off everything, in this case only vdW 45 | couple-intramol = no 46 | ; Vectors of lambda specified here 47 | ; Each combination is an index that is retrieved from init_lambda_state for each simulation 48 | ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 49 | vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 50 | coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 51 | ; We are not transforming any bonded or restrained interactions 52 | bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 53 | restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 54 | ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) 55 | mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 56 | ; Not doing simulated temperting here 57 | temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 58 | ; Options for the decoupling 59 | sc-alpha = 0.5 60 | sc-coul = no ; linear interpolation of Coulomb (none in this case) 61 | sc-power = 1 62 | sc-sigma = 0.3 63 | nstdhdl = 10 64 | ; No velocities during EM 65 | gen_vel = no 66 | ; options for bonds 67 | constraints = h-bonds ; we only have C-H bonds here 68 | ; Type of constraint algorithm 69 | constraint-algorithm = lincs 70 | ; Do not constrain the starting configuration 71 | continuation = no 72 | ; Highest order in the expansion of the constraint coupling matrix 73 | lincs-order = 12 74 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/job.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Set some environment variables 4 | FREE_ENERGY=`pwd` 5 | echo "Free energy home directory set to $FREE_ENERGY" 6 | MDP=$FREE_ENERGY/MDP 7 | echo ".mdp files are stored in $MDP" 8 | 9 | # Change to the location of your GROMACS-2018 installation 10 | GMX=/usr/local/gromacs/bin 11 | 12 | for (( i=0; i<21; i++ )) 13 | do 14 | LAMBDA=$i 15 | 16 | # A new directory will be created for each value of lambda and 17 | # at each step in the workflow for maximum organization. 18 | 19 | mkdir Lambda_$LAMBDA 20 | cd Lambda_$LAMBDA 21 | 22 | ############################## 23 | # ENERGY MINIMIZATION STEEP # 24 | ############################## 25 | echo "Starting minimization for lambda = $LAMBDA..." 26 | 27 | mkdir EM 28 | cd EM 29 | 30 | # Iterative calls to grompp and mdrun to run the simulations 31 | 32 | $GMX/gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/methane_water.gro -p $FREE_ENERGY/topol.top -o min$LAMBDA.tpr 33 | 34 | $GMX/gmx mdrun -deffnm min$LAMBDA 35 | 36 | sleep 10 37 | 38 | ##################### 39 | # NVT EQUILIBRATION # 40 | ##################### 41 | echo "Starting constant volume equilibration..." 42 | 43 | cd ../ 44 | mkdir NVT 45 | cd NVT 46 | 47 | $GMX/gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/topol.top -o nvt$LAMBDA.tpr 48 | 49 | $GMX/gmx mdrun -deffnm nvt$LAMBDA 50 | 51 | echo "Constant volume equilibration complete." 52 | 53 | sleep 10 54 | 55 | ##################### 56 | # NPT EQUILIBRATION # 57 | ##################### 58 | echo "Starting constant pressure equilibration..." 59 | 60 | cd ../ 61 | mkdir NPT 62 | cd NPT 63 | 64 | $GMX/gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr 65 | 66 | $GMX/gmx mdrun -deffnm npt$LAMBDA 67 | 68 | echo "Constant pressure equilibration complete." 69 | 70 | sleep 10 71 | 72 | ################# 73 | # PRODUCTION MD # 74 | ################# 75 | echo "Starting production MD simulation..." 76 | 77 | cd ../ 78 | mkdir Production_MD 79 | cd Production_MD 80 | 81 | $GMX/gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr 82 | 83 | $GMX/gmx mdrun -deffnm md$LAMBDA 84 | 85 | echo "Production MD complete." 86 | 87 | # End 88 | echo "Ending. Job completed for lambda = $LAMBDA" 89 | 90 | cd $FREE_ENERGY 91 | done 92 | 93 | exit; 94 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/md.mdp: -------------------------------------------------------------------------------- 1 | ; Run control 2 | integrator = sd ; Langevin dynamics 3 | tinit = 0 4 | dt = 0.002 5 | nsteps = 500000 ; 1 ns 6 | nstcomm = 100 7 | ; Output control 8 | nstxout = 500 9 | nstvout = 500 10 | nstfout = 0 11 | nstlog = 500 12 | nstenergy = 500 13 | nstxout-compressed = 0 14 | ; Neighborsearching and short-range nonbonded interactions 15 | cutoff-scheme = verlet 16 | nstlist = 20 17 | ns_type = grid 18 | pbc = xyz 19 | rlist = 1.2 20 | ; Electrostatics 21 | coulombtype = PME 22 | rcoulomb = 1.2 23 | ; van der Waals 24 | vdwtype = cutoff 25 | vdw-modifier = potential-switch 26 | rvdw-switch = 1.0 27 | rvdw = 1.2 28 | ; Apply long range dispersion corrections for Energy and Pressure 29 | DispCorr = EnerPres 30 | ; Spacing for the PME/PPPM FFT grid 31 | fourierspacing = 0.12 32 | ; EWALD/PME/PPPM parameters 33 | pme_order = 6 34 | ewald_rtol = 1e-06 35 | epsilon_surface = 0 36 | ; Temperature coupling 37 | ; tcoupl is implicitly handled by the sd integrator 38 | tc_grps = system 39 | tau_t = 1.0 40 | ref_t = 298 41 | ; Pressure coupling is on for NPT 42 | Pcoupl = Parrinello-Rahman 43 | tau_p = 1.0 44 | compressibility = 4.5e-05 45 | ref_p = 1.0 46 | ; Free energy control stuff 47 | free_energy = yes 48 | init_lambda_state = 0 49 | delta_lambda = 0 50 | calc_lambda_neighbors = 1 ; only immediate neighboring windows 51 | couple-moltype = Methane ; name of moleculetype to decouple 52 | couple-lambda0 = vdw ; only van der Waals interactions 53 | couple-lambda1 = none ; turn off everything, in this case only vdW 54 | couple-intramol = no 55 | ; Vectors of lambda specified here 56 | ; Each combination is an index that is retrieved from init_lambda_state for each simulation 57 | ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 58 | vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 59 | coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60 | ; We are not transforming any bonded or restrained interactions 61 | bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 62 | restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 63 | ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) 64 | mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 65 | ; Not doing simulated temperting here 66 | temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 67 | ; Options for the decoupling 68 | sc-alpha = 0.5 69 | sc-coul = no ; linear interpolation of Coulomb (none in this case) 70 | sc-power = 1 71 | sc-sigma = 0.3 72 | nstdhdl = 10 73 | ; Do not generate velocities 74 | gen_vel = no 75 | ; options for bonds 76 | constraints = h-bonds ; we only have C-H bonds here 77 | ; Type of constraint algorithm 78 | constraint-algorithm = lincs 79 | ; Constrain the starting configuration 80 | ; since we are continuing from NPT 81 | continuation = yes 82 | ; Highest order in the expansion of the constraint coupling matrix 83 | lincs-order = 12 84 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/mdout.mdp: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'mdout.mdp' was generated 3 | ; By user: jalemkul (502) 4 | ; On host: BC-Eng303-001.local 5 | ; At date: Tue Jun 19 14:38:57 2018 6 | 7 | ; 8 | ; Created by: 9 | ; :-) GROMACS - gmx grompp, 2016.3 (-: 10 | ; 11 | ; Executable: /usr/local/gromacs/bin/gmx 12 | ; Data prefix: /usr/local/gromacs 13 | ; Working dir: /Users/jalemkul/Web/Bevan_Lab_Site/justin/gmx-tutorials/free_energy/Files 14 | ; Command line: 15 | ; gmx grompp -f em_steep.mdp -c methane_water.gro -p topol.top -o test.tpr 16 | 17 | ; VARIOUS PREPROCESSING OPTIONS 18 | ; Preprocessor information: use cpp syntax. 19 | ; e.g.: -I/home/joe/doe -I/home/mary/roe 20 | include = 21 | ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) 22 | define = 23 | 24 | ; RUN CONTROL PARAMETERS 25 | integrator = steep 26 | ; Start time and timestep in ps 27 | tinit = 0 28 | dt = 0.001 29 | nsteps = 5000 30 | ; For exact run continuation or redoing part of a run 31 | init-step = 0 32 | ; Part index is updated automatically on checkpointing (keeps files separate) 33 | simulation-part = 1 34 | ; mode for center of mass motion removal 35 | comm-mode = Linear 36 | ; number of steps for center of mass motion removal 37 | nstcomm = 100 38 | ; group(s) for center of mass motion removal 39 | comm-grps = 40 | 41 | ; LANGEVIN DYNAMICS OPTIONS 42 | ; Friction coefficient (amu/ps) and random seed 43 | bd-fric = 0 44 | ld-seed = -1 45 | 46 | ; ENERGY MINIMIZATION OPTIONS 47 | ; Force tolerance and initial step-size 48 | emtol = 100 49 | emstep = 0.01 50 | ; Max number of iterations in relax-shells 51 | niter = 20 52 | ; Step size (ps^2) for minimization of flexible constraints 53 | fcstep = 0 54 | ; Frequency of steepest descents steps when doing CG 55 | nstcgsteep = 1000 56 | nbfgscorr = 10 57 | 58 | ; TEST PARTICLE INSERTION OPTIONS 59 | rtpi = 0.05 60 | 61 | ; OUTPUT CONTROL OPTIONS 62 | ; Output frequency for coords (x), velocities (v) and forces (f) 63 | nstxout = 0 64 | nstvout = 0 65 | nstfout = 0 66 | ; Output frequency for energies to log file and energy file 67 | nstlog = 1 68 | nstcalcenergy = 100 69 | nstenergy = 1 70 | ; Output frequency and precision for .xtc file 71 | nstxout-compressed = 0 72 | compressed-x-precision = 1000 73 | ; This selects the subset of atoms for the compressed 74 | ; trajectory file. You can select multiple groups. By 75 | ; default, all atoms will be written. 76 | compressed-x-grps = 77 | ; Selection of energy groups 78 | energygrps = 79 | 80 | ; NEIGHBORSEARCHING PARAMETERS 81 | ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) 82 | cutoff-scheme = verlet 83 | ; nblist update frequency 84 | nstlist = 1 85 | ; ns algorithm (simple or grid) 86 | ns_type = grid 87 | ; Periodic boundary conditions: xyz, no, xy 88 | pbc = xyz 89 | periodic-molecules = no 90 | ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, 91 | ; a value of -1 means: use rlist 92 | verlet-buffer-tolerance = 0.005 93 | ; nblist cut-off 94 | rlist = 1.2 95 | ; long-range cut-off for switched potentials 96 | 97 | ; OPTIONS FOR ELECTROSTATICS AND VDW 98 | ; Method for doing electrostatics 99 | coulombtype = PME 100 | coulomb-modifier = Potential-shift-Verlet 101 | rcoulomb-switch = 0 102 | rcoulomb = 1.2 103 | ; Relative dielectric constant for the medium and the reaction field 104 | epsilon-r = 1 105 | epsilon-rf = 0 106 | ; Method for doing Van der Waals 107 | vdwtype = cutoff 108 | vdw-modifier = potential-switch 109 | ; cut-off lengths 110 | rvdw-switch = 1.0 111 | rvdw = 1.2 112 | ; Apply long range dispersion corrections for Energy and Pressure 113 | DispCorr = EnerPres 114 | ; Extension of the potential lookup tables beyond the cut-off 115 | table-extension = 1 116 | ; Separate tables between energy group pairs 117 | energygrp-table = 118 | ; Spacing for the PME/PPPM FFT grid 119 | fourierspacing = 0.12 120 | ; FFT grid size, when a value is 0 fourierspacing will be used 121 | fourier-nx = 0 122 | fourier-ny = 0 123 | fourier-nz = 0 124 | ; EWALD/PME/PPPM parameters 125 | pme_order = 6 126 | ewald_rtol = 1e-06 127 | ewald-rtol-lj = 0.001 128 | lj-pme-comb-rule = Geometric 129 | ewald-geometry = 3d 130 | epsilon_surface = 0 131 | 132 | ; IMPLICIT SOLVENT ALGORITHM 133 | implicit-solvent = No 134 | 135 | ; GENERALIZED BORN ELECTROSTATICS 136 | ; Algorithm for calculating Born radii 137 | gb-algorithm = Still 138 | ; Frequency of calculating the Born radii inside rlist 139 | nstgbradii = 1 140 | ; Cutoff for Born radii calculation; the contribution from atoms 141 | ; between rlist and rgbradii is updated every nstlist steps 142 | rgbradii = 1 143 | ; Dielectric coefficient of the implicit solvent 144 | gb-epsilon-solvent = 80 145 | ; Salt concentration in M for Generalized Born models 146 | gb-saltconc = 0 147 | ; Scaling factors used in the OBC GB model. Default values are OBC(II) 148 | gb-obc-alpha = 1 149 | gb-obc-beta = 0.8 150 | gb-obc-gamma = 4.85 151 | gb-dielectric-offset = 0.009 152 | sa-algorithm = Ace-approximation 153 | ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA 154 | ; The value -1 will set default value for Still/HCT/OBC GB-models. 155 | sa-surface-tension = -1 156 | 157 | ; OPTIONS FOR WEAK COUPLING ALGORITHMS 158 | ; Temperature coupling 159 | tcoupl = no 160 | nsttcouple = -1 161 | nh-chain-length = 10 162 | print-nose-hoover-chain-variables = no 163 | ; Groups to couple separately 164 | tc-grps = 165 | ; Time constant (ps) and reference temperature (K) 166 | tau-t = 167 | ref-t = 168 | ; pressure coupling 169 | pcoupl = no 170 | pcoupltype = Isotropic 171 | nstpcouple = -1 172 | ; Time constant (ps), compressibility (1/bar) and reference P (bar) 173 | tau-p = 1 174 | compressibility = 175 | ref-p = 176 | ; Scaling of reference coordinates, No, All or COM 177 | refcoord-scaling = No 178 | 179 | ; OPTIONS FOR QMMM calculations 180 | QMMM = no 181 | ; Groups treated Quantum Mechanically 182 | QMMM-grps = 183 | ; QM method 184 | QMmethod = 185 | ; QMMM scheme 186 | QMMMscheme = normal 187 | ; QM basisset 188 | QMbasis = 189 | ; QM charge 190 | QMcharge = 191 | ; QM multiplicity 192 | QMmult = 193 | ; Surface Hopping 194 | SH = 195 | ; CAS space options 196 | CASorbitals = 197 | CASelectrons = 198 | SAon = 199 | SAoff = 200 | SAsteps = 201 | ; Scale factor for MM charges 202 | MMChargeScaleFactor = 1 203 | ; Optimization of QM subsystem 204 | bOPT = 205 | bTS = 206 | 207 | ; SIMULATED ANNEALING 208 | ; Type of annealing for each temperature group (no/single/periodic) 209 | annealing = 210 | ; Number of time points to use for specifying annealing in each group 211 | annealing-npoints = 212 | ; List of times at the annealing points for each group 213 | annealing-time = 214 | ; Temp. at each annealing point, for each group. 215 | annealing-temp = 216 | 217 | ; GENERATE VELOCITIES FOR STARTUP RUN 218 | gen_vel = no 219 | gen-temp = 300 220 | gen-seed = -1 221 | 222 | ; OPTIONS FOR BONDS 223 | constraints = h-bonds 224 | ; Type of constraint algorithm 225 | constraint-algorithm = lincs 226 | ; Do not constrain the start configuration 227 | continuation = no 228 | ; Use successive overrelaxation to reduce the number of shake iterations 229 | Shake-SOR = no 230 | ; Relative tolerance of shake 231 | shake-tol = 0.0001 232 | ; Highest order in the expansion of the constraint coupling matrix 233 | lincs-order = 12 234 | ; Number of iterations in the final step of LINCS. 1 is fine for 235 | ; normal simulations, but use 2 to conserve energy in NVE runs. 236 | ; For energy minimization with constraints it should be 4 to 8. 237 | lincs-iter = 1 238 | ; Lincs will write a warning to the stderr if in one step a bond 239 | ; rotates over more degrees than 240 | lincs-warnangle = 30 241 | ; Convert harmonic bonds to morse potentials 242 | morse = no 243 | 244 | ; ENERGY GROUP EXCLUSIONS 245 | ; Pairs of energy groups for which all non-bonded interactions are excluded 246 | energygrp-excl = 247 | 248 | ; WALLS 249 | ; Number of walls, type, atom types, densities and box-z scale factor for Ewald 250 | nwall = 0 251 | wall-type = 9-3 252 | wall-r-linpot = -1 253 | wall-atomtype = 254 | wall-density = 255 | wall-ewald-zfac = 3 256 | 257 | ; COM PULLING 258 | pull = no 259 | 260 | ; ENFORCED ROTATION 261 | ; Enforced rotation: No or Yes 262 | rotation = no 263 | 264 | ; Group to display and/or manipulate in interactive MD session 265 | IMD-group = 266 | 267 | ; NMR refinement stuff 268 | ; Distance restraints type: No, Simple or Ensemble 269 | disre = No 270 | ; Force weighting of pairs in one distance restraint: Conservative or Equal 271 | disre-weighting = Conservative 272 | ; Use sqrt of the time averaged times the instantaneous violation 273 | disre-mixed = no 274 | disre-fc = 1000 275 | disre-tau = 0 276 | ; Output frequency for pair distances to energy file 277 | nstdisreout = 100 278 | ; Orientation restraints: No or Yes 279 | orire = no 280 | ; Orientation restraints force constant and tau for time averaging 281 | orire-fc = 0 282 | orire-tau = 0 283 | orire-fitgrp = 284 | ; Output frequency for trace(SD) and S to energy file 285 | nstorireout = 100 286 | 287 | ; Free energy variables 288 | free_energy = yes 289 | couple-moltype = Methane 290 | couple-lambda0 = vdw 291 | couple-lambda1 = none 292 | couple-intramol = no 293 | init-lambda = -1 294 | init_lambda_state = 0 295 | delta_lambda = 0 296 | nstdhdl = 10 297 | fep-lambdas = 298 | mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 299 | coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 300 | vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 301 | bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 302 | restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 303 | temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 304 | calc_lambda_neighbors = 1 305 | init-lambda-weights = 306 | dhdl-print-energy = no 307 | sc-alpha = 0.5 308 | sc-power = 1 309 | sc-r-power = 6 310 | sc-sigma = 0.3 311 | sc-coul = no 312 | separate-dhdl-file = yes 313 | dhdl-derivatives = yes 314 | dh_hist_size = 0 315 | dh_hist_spacing = 0.1 316 | 317 | ; Non-equilibrium MD stuff 318 | acc-grps = 319 | accelerate = 320 | freezegrps = 321 | freezedim = 322 | cos-acceleration = 0 323 | deform = 324 | 325 | ; simulated tempering variables 326 | simulated-tempering = no 327 | simulated-tempering-scaling = geometric 328 | sim-temp-low = 300 329 | sim-temp-high = 300 330 | 331 | ; Electric fields 332 | ; Format is number of terms (int) and for all terms an amplitude (real) 333 | ; and a phase angle (real) 334 | E-x = 335 | ; Time dependent (pulsed) electric field. Format is omega, time for pulse 336 | ; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving 337 | ; the field to be a cosine function. 338 | E-xt = 339 | E-y = 340 | E-yt = 341 | E-z = 342 | E-zt = 343 | 344 | ; Ion/water position swapping for computational electrophysiology setups 345 | ; Swap positions along direction: no, X, Y, Z 346 | swapcoords = no 347 | adress = no 348 | 349 | ; User defined thingies 350 | user1-grps = 351 | user2-grps = 352 | userint1 = 0 353 | userint2 = 0 354 | userint3 = 0 355 | userint4 = 0 356 | userreal1 = 0 357 | userreal2 = 0 358 | userreal3 = 0 359 | userreal4 = 0 360 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/npt.mdp: -------------------------------------------------------------------------------- 1 | ; Run control 2 | integrator = sd ; Langevin dynamics 3 | tinit = 0 4 | dt = 0.002 5 | nsteps = 50000 ; 100 ps 6 | nstcomm = 100 7 | ; Output control 8 | nstxout = 500 9 | nstvout = 500 10 | nstfout = 0 11 | nstlog = 500 12 | nstenergy = 500 13 | nstxout-compressed = 0 14 | ; Neighborsearching and short-range nonbonded interactions 15 | cutoff-scheme = verlet 16 | nstlist = 20 17 | ns_type = grid 18 | pbc = xyz 19 | rlist = 1.2 20 | ; Electrostatics 21 | coulombtype = PME 22 | rcoulomb = 1.2 23 | ; van der Waals 24 | vdwtype = cutoff 25 | vdw-modifier = potential-switch 26 | rvdw-switch = 1.0 27 | rvdw = 1.2 28 | ; Apply long range dispersion corrections for Energy and Pressure 29 | DispCorr = EnerPres 30 | ; Spacing for the PME/PPPM FFT grid 31 | fourierspacing = 0.12 32 | ; EWALD/PME/PPPM parameters 33 | pme_order = 6 34 | ewald_rtol = 1e-06 35 | epsilon_surface = 0 36 | ; Temperature coupling 37 | ; tcoupl is implicitly handled by the sd integrator 38 | tc_grps = system 39 | tau_t = 1.0 40 | ref_t = 298 41 | ; Pressure coupling is on for NPT 42 | Pcoupl = Parrinello-Rahman 43 | tau_p = 1.0 44 | compressibility = 4.5e-05 45 | ref_p = 1.0 46 | ; Free energy control stuff 47 | free_energy = yes 48 | init_lambda_state = 0 49 | delta_lambda = 0 50 | calc_lambda_neighbors = 1 ; only immediate neighboring windows 51 | couple-moltype = Methane ; name of moleculetype to decouple 52 | couple-lambda0 = vdw ; only van der Waals interactions 53 | couple-lambda1 = none ; turn off everything, in this case only vdW 54 | couple-intramol = no 55 | ; Vectors of lambda specified here 56 | ; Each combination is an index that is retrieved from init_lambda_state for each simulation 57 | ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 58 | vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 59 | coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60 | ; We are not transforming any bonded or restrained interactions 61 | bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 62 | restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 63 | ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) 64 | mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 65 | ; Not doing simulated temperting here 66 | temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 67 | ; Options for the decoupling 68 | sc-alpha = 0.5 69 | sc-coul = no ; linear interpolation of Coulomb (none in this case) 70 | sc-power = 1 71 | sc-sigma = 0.3 72 | nstdhdl = 10 73 | ; Do not generate velocities 74 | gen_vel = no 75 | ; options for bonds 76 | constraints = h-bonds ; we only have C-H bonds here 77 | ; Type of constraint algorithm 78 | constraint-algorithm = lincs 79 | ; Constrain the starting configuration 80 | ; since we are continuing from NVT 81 | continuation = yes 82 | ; Highest order in the expansion of the constraint coupling matrix 83 | lincs-order = 12 84 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/nvt.mdp: -------------------------------------------------------------------------------- 1 | ; Run control 2 | integrator = sd ; Langevin dynamics 3 | tinit = 0 4 | dt = 0.002 5 | nsteps = 50000 ; 100 ps 6 | nstcomm = 100 7 | ; Output control 8 | nstxout = 500 9 | nstvout = 500 10 | nstfout = 0 11 | nstlog = 500 12 | nstenergy = 500 13 | nstxout-compressed = 0 14 | ; Neighborsearching and short-range nonbonded interactions 15 | cutoff-scheme = verlet 16 | nstlist = 20 17 | ns_type = grid 18 | pbc = xyz 19 | rlist = 1.2 20 | ; Electrostatics 21 | coulombtype = PME 22 | rcoulomb = 1.2 23 | ; van der Waals 24 | vdwtype = cutoff 25 | vdw-modifier = potential-switch 26 | rvdw-switch = 1.0 27 | rvdw = 1.2 28 | ; Apply long range dispersion corrections for Energy and Pressure 29 | DispCorr = EnerPres 30 | ; Spacing for the PME/PPPM FFT grid 31 | fourierspacing = 0.12 32 | ; EWALD/PME/PPPM parameters 33 | pme_order = 6 34 | ewald_rtol = 1e-06 35 | epsilon_surface = 0 36 | ; Temperature coupling 37 | ; tcoupl is implicitly handled by the sd integrator 38 | tc_grps = system 39 | tau_t = 1.0 40 | ref_t = 298 41 | ; Pressure coupling is off for NVT 42 | Pcoupl = No 43 | tau_p = 0.5 44 | compressibility = 4.5e-05 45 | ref_p = 1.0 46 | ; Free energy control stuff 47 | free_energy = yes 48 | init_lambda_state = 0 49 | delta_lambda = 0 50 | calc_lambda_neighbors = 1 ; only immediate neighboring windows 51 | couple-moltype = Methane ; name of moleculetype to decouple 52 | couple-lambda0 = vdw ; only van der Waals interactions 53 | couple-lambda1 = none ; turn off everything, in this case only vdW 54 | couple-intramol = no 55 | ; Vectors of lambda specified here 56 | ; Each combination is an index that is retrieved from init_lambda_state for each simulation 57 | ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 58 | vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 59 | coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60 | ; We are not transforming any bonded or restrained interactions 61 | bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 62 | restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 63 | ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) 64 | mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 65 | ; Not doing simulated temperting here 66 | temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 67 | ; Options for the decoupling 68 | sc-alpha = 0.5 69 | sc-coul = no ; linear interpolation of Coulomb (none in this case) 70 | sc-power = 1 71 | sc-sigma = 0.3 72 | nstdhdl = 10 73 | ; Generate velocities to start 74 | gen_vel = yes 75 | gen_temp = 300 76 | gen_seed = -1 77 | ; options for bonds 78 | constraints = h-bonds ; we only have C-H bonds here 79 | ; Type of constraint algorithm 80 | constraint-algorithm = lincs 81 | ; Do not constrain the starting configuration 82 | continuation = no 83 | ; Highest order in the expansion of the constraint coupling matrix 84 | lincs-order = 12 85 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/test.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/tutorial-files/free_energy/test.tpr -------------------------------------------------------------------------------- /tutorial-files/free_energy/topol.top: -------------------------------------------------------------------------------- 1 | ; Topology for methane in TIP3P 2 | 3 | #include "oplsaa.ff/forcefield.itp" 4 | 5 | [ moleculetype ] 6 | ; Name nrexcl 7 | Methane 3 8 | 9 | [ atoms ] 10 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 11 | 1 opls_138 1 ALAB CB 1 0.000 12.011 12 | 2 opls_140 1 ALAB HB1 2 0.000 1.008 13 | 3 opls_140 1 ALAB HB2 3 0.000 1.008 14 | 4 opls_140 1 ALAB HB3 4 0.000 1.008 15 | 5 opls_140 1 ALAB HB4 5 0.000 1.008 16 | 17 | 18 | 19 | [ bonds ] 20 | ; ai aj funct c0 c1 c2 c3 21 | 1 2 1 22 | 1 3 1 23 | 1 4 1 24 | 1 5 1 25 | 26 | [ angles ] 27 | ; ai aj ak funct c0 c1 c2 c3 28 | 2 1 3 1 29 | 2 1 4 1 30 | 2 1 5 1 31 | 3 1 4 1 32 | 3 1 5 1 33 | 4 1 5 1 34 | 35 | ; water topology 36 | #include "oplsaa.ff/tip3p.itp" 37 | 38 | [ system ] 39 | ; Name 40 | Methane in water 41 | 42 | [ molecules ] 43 | ; Compound #mols 44 | Methane 1 45 | SOL 596 46 | -------------------------------------------------------------------------------- /tutorial-files/free_energy/write_mdp.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl -w 2 | 3 | use strict; 4 | 5 | # opens a generic .mdp file and replaces the values of 6 | # 'init_lambda_state' with values at increments of 1 7 | 8 | unless (@ARGV) { 9 | die "Usage: $0 input.mdp\n"; 10 | } 11 | 12 | my $mdp = $ARGV[0]; 13 | 14 | my @temp = split('\.', $mdp); 15 | my $base = $temp[0]; 16 | 17 | open(IN, "<$mdp"); 18 | my @in = ; 19 | close(IN); 20 | 21 | # note we are specifying indices for states, not actual lambda values like in previous versions 22 | for (my $i=0; $i<21; $i++) { 23 | 24 | my $filename = "${base}_${i}.mdp"; 25 | 26 | open(OUT, ">$filename"); 27 | 28 | foreach $_ (@in) { 29 | unless ($_ =~ /^init_lambda_state/) { 30 | print OUT $_; 31 | } 32 | 33 | if ($_ =~ /^init_lambda_state\s*=/) { 34 | printf OUT "%s %d\n", $&, $i; 35 | } 36 | } 37 | 38 | close(OUT); 39 | 40 | } 41 | 42 | exit; 43 | -------------------------------------------------------------------------------- /tutorial-files/lysozyme/ions.mdp: -------------------------------------------------------------------------------- 1 | ; ions.mdp - used as input into grompp to generate ions.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Minimization step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | cutoff-scheme = Verlet ; Buffered neighbor searching 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 13 | rcoulomb = 1.0 ; Short-range electrostatic cut-off 14 | rvdw = 1.0 ; Short-range Van der Waals cut-off 15 | pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions 16 | -------------------------------------------------------------------------------- /tutorial-files/lysozyme/md.mdp: -------------------------------------------------------------------------------- 1 | title = OPLS Lysozyme NPT equilibration 2 | ; Run parameters 3 | integrator = md ; leap-frog integrator 4 | nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) 5 | dt = 0.002 ; 2 fs 6 | ; Output control 7 | nstxout = 0 ; suppress bulky .trr file by specifying 8 | nstvout = 0 ; 0 for output frequency of nstxout, 9 | nstfout = 0 ; nstvout, and nstfout 10 | nstenergy = 5000 ; save energies every 10.0 ps 11 | nstlog = 5000 ; update log file every 10.0 ps 12 | nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps 13 | compressed-x-grps = System ; save the whole system 14 | ; Bond parameters 15 | continuation = yes ; Restarting after NPT 16 | constraint_algorithm = lincs ; holonomic constraints 17 | constraints = h-bonds ; bonds involving H are constrained 18 | lincs_iter = 1 ; accuracy of LINCS 19 | lincs_order = 4 ; also related to accuracy 20 | ; Neighborsearching 21 | cutoff-scheme = Verlet ; Buffered neighbor searching 22 | ns_type = grid ; search neighboring grid cells 23 | nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme 24 | rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) 25 | rvdw = 1.0 ; short-range van der Waals cutoff (in nm) 26 | ; Electrostatics 27 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 28 | pme_order = 4 ; cubic interpolation 29 | fourierspacing = 0.16 ; grid spacing for FFT 30 | ; Temperature coupling is on 31 | tcoupl = V-rescale ; modified Berendsen thermostat 32 | tc-grps = Protein Non-Protein ; two coupling groups - more accurate 33 | tau_t = 0.1 0.1 ; time constant, in ps 34 | ref_t = 300 300 ; reference temperature, one for each group, in K 35 | ; Pressure coupling is on 36 | pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 37 | pcoupltype = isotropic ; uniform scaling of box vectors 38 | tau_p = 2.0 ; time constant, in ps 39 | ref_p = 1.0 ; reference pressure, in bar 40 | compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 41 | ; Periodic boundary conditions 42 | pbc = xyz ; 3-D PBC 43 | ; Dispersion correction 44 | DispCorr = EnerPres ; account for cut-off vdW scheme 45 | ; Velocity generation 46 | gen_vel = no ; Velocity generation is off 47 | -------------------------------------------------------------------------------- /tutorial-files/lysozyme/minim.mdp: -------------------------------------------------------------------------------- 1 | ; minim.mdp - used as input into grompp to generate em.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Minimization step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | cutoff-scheme = Verlet ; Buffered neighbor searching 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | coulombtype = PME ; Treatment of long range electrostatic interactions 13 | rcoulomb = 1.0 ; Short-range electrostatic cut-off 14 | rvdw = 1.0 ; Short-range Van der Waals cut-off 15 | pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions 16 | -------------------------------------------------------------------------------- /tutorial-files/lysozyme/npt.mdp: -------------------------------------------------------------------------------- 1 | title = OPLS Lysozyme NPT equilibration 2 | define = -DPOSRES ; position restrain the protein 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstxout = 500 ; save coordinates every 1.0 ps 9 | nstvout = 500 ; save velocities every 1.0 ps 10 | nstenergy = 500 ; save energies every 1.0 ps 11 | nstlog = 500 ; update log file every 1.0 ps 12 | ; Bond parameters 13 | continuation = yes ; Restarting after NVT 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = h-bonds ; bonds involving H are constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Nonbonded settings 19 | cutoff-scheme = Verlet ; Buffered neighbor searching 20 | ns_type = grid ; search neighboring grid cells 21 | nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme 22 | rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.0 ; short-range van der Waals cutoff (in nm) 24 | DispCorr = EnerPres ; account for cut-off vdW scheme 25 | ; Electrostatics 26 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 27 | pme_order = 4 ; cubic interpolation 28 | fourierspacing = 0.16 ; grid spacing for FFT 29 | ; Temperature coupling is on 30 | tcoupl = V-rescale ; modified Berendsen thermostat 31 | tc-grps = Protein Non-Protein ; two coupling groups - more accurate 32 | tau_t = 0.1 0.1 ; time constant, in ps 33 | ref_t = 300 300 ; reference temperature, one for each group, in K 34 | ; Pressure coupling is on 35 | pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 36 | pcoupltype = isotropic ; uniform scaling of box vectors 37 | tau_p = 2.0 ; time constant, in ps 38 | ref_p = 1.0 ; reference pressure, in bar 39 | compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 40 | refcoord_scaling = com 41 | ; Periodic boundary conditions 42 | pbc = xyz ; 3-D PBC 43 | ; Velocity generation 44 | gen_vel = no ; Velocity generation is off 45 | -------------------------------------------------------------------------------- /tutorial-files/lysozyme/nvt.mdp: -------------------------------------------------------------------------------- 1 | title = OPLS Lysozyme NVT equilibration 2 | define = -DPOSRES ; position restrain the protein 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstxout = 500 ; save coordinates every 1.0 ps 9 | nstvout = 500 ; save velocities every 1.0 ps 10 | nstenergy = 500 ; save energies every 1.0 ps 11 | nstlog = 500 ; update log file every 1.0 ps 12 | ; Bond parameters 13 | continuation = no ; first dynamics run 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = h-bonds ; bonds involving H are constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Nonbonded settings 19 | cutoff-scheme = Verlet ; Buffered neighbor searching 20 | ns_type = grid ; search neighboring grid cells 21 | nstlist = 10 ; 20 fs, largely irrelevant with Verlet 22 | rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.0 ; short-range van der Waals cutoff (in nm) 24 | DispCorr = EnerPres ; account for cut-off vdW scheme 25 | ; Electrostatics 26 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 27 | pme_order = 4 ; cubic interpolation 28 | fourierspacing = 0.16 ; grid spacing for FFT 29 | ; Temperature coupling is on 30 | tcoupl = V-rescale ; modified Berendsen thermostat 31 | tc-grps = Protein Non-Protein ; two coupling groups - more accurate 32 | tau_t = 0.1 0.1 ; time constant, in ps 33 | ref_t = 300 300 ; reference temperature, one for each group, in K 34 | ; Pressure coupling is off 35 | pcoupl = no ; no pressure coupling in NVT 36 | ; Periodic boundary conditions 37 | pbc = xyz ; 3-D PBC 38 | ; Velocity generation 39 | gen_vel = yes ; assign velocities from Maxwell distribution 40 | gen_temp = 300 ; temperature for Maxwell distribution 41 | gen_seed = -1 ; generate a random seed 42 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/anneal_npt.mdp: -------------------------------------------------------------------------------- 1 | title = Simulated Annealing 2 | define = -DPOSRES -DPOSRES_LIPID ; restrain protein and lipid P8 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | dt = 0.002 ; 2 fs 6 | nsteps = 250000 ; 500 ps 7 | ; Bond parameters 8 | continuation = no ; starting up 9 | constraints = all-bonds ; constrain all bond lengths 10 | constraint-algorithm = lincs ; holonomic constraints 11 | lincs-iter = 1 ; accuracy of LINCS 12 | lincs-order = 4 ; also related to accuracy 13 | ; Output control 14 | nstxout = 1000 ; save coordinates every 2 ps 15 | nstvout = 1000 ; save velocities every 2 ps 16 | nstfout = 1000 ; save forces every 2 ps 17 | nstenergy = 1000 ; save energies every 2 ps 18 | ; Neighborsearching 19 | nstlist = 5 ; 10 fs 20 | ns_type = grid ; search neighboring grid cells 21 | rlist = 1.2 ; short-range neighborlist cutoff (nm) 22 | rcoulomb = 1.2 ; short-range electrostatic cutoff (nm) 23 | rvdw = 1.2 ; short-range van der Waals cutoff (nm) 24 | ; Electrostatics 25 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 26 | pme_order = 4 ; cubic interpolation 27 | fourierspacing = 0.16 ; grid spacing for FFT 28 | ; Temperature coupling is on in three groups 29 | Tcoupl = Berendsen ; Weak coupling 30 | tc_grps = Protein_DPPC Water_and_ions ; two groups - more accurate 31 | tau_t = 0.1 0.1 ; time constant, in ps 32 | ref_t = 323 323 ; reference temperature, one for each group, in K 33 | ; Pressure coupling 34 | Pcoupl = Berendsen ; Weak coupling 35 | Pcoupltype = semiisotropic ; uniform scaling of x-y vectors, independent z 36 | ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) 37 | compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 38 | ; Generate velocities is off 39 | gen_vel = no ; Velocity generation is off 40 | ; Periodic boundary conditions are on in all directions 41 | pbc = xyz ; 3-D PBC 42 | ; Dispersion correction 43 | DispCorr = EnerPres ; account for cut-off vdW scheme 44 | ; COM motion removal 45 | ; These options remove motion of the protein/bilayer relative to the solvent/ions 46 | nstcomm = 1 47 | comm-mode = Linear 48 | comm-grps = Protein_DPPC Water_and_ions 49 | ; Simulated annealing 50 | annealing = single single single ; single sequence of points for each T-coupling group 51 | annealing_npoints = 2 2 2 ; two points - start and end temperatures 52 | annealing_time = 0 500 0 500 0 500 ; time frame of heating - heat over period of 500 ps 53 | annealing_temp = 0 323 0 323 0 323 ; start and end temperatures 54 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/ions.mdp: -------------------------------------------------------------------------------- 1 | ; ions.mdp - used as input into grompp to generate ions.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Minimization step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | cutoff-scheme = Verlet ; Buffered neighbor searching 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | rlist = 1.2 ; Cut-off for making neighbor list (short range forces) 13 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 14 | rcoulomb = 1.2 ; Short-range electrostatic cut-off 15 | rvdw = 1.2 ; Short-range Van der Waals cut-off 16 | pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions 17 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/lipid_posre.itp: -------------------------------------------------------------------------------- 1 | ; position restraint file for DPPC P8 2 | 3 | [ position_restraints ] 4 | ; i funct fcx fcy fcz 5 | 8 1 0 0 1000 6 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/md.mdp: -------------------------------------------------------------------------------- 1 | title = KALP15-DPPC Production MD 2 | ; Run parameters 3 | integrator = md ; leap-frog integrator 4 | nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) 5 | dt = 0.002 ; 2 fs 6 | ; Output control 7 | nstxout = 1000 ; save coordinates every 2 ps 8 | nstvout = 1000 ; save velocities every 2 ps 9 | nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps 10 | nstenergy = 1000 ; save energies every 2 ps 11 | nstlog = 1000 ; update log file every 2 ps 12 | ; Bond parameters 13 | continuation = yes ; Restarting after NPT 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Neighborsearching 19 | ns_type = grid ; search neighboring grid cels 20 | nstlist = 5 ; 10 fs 21 | rlist = 1.2 ; short-range neighborlist cutoff (in nm) 22 | rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 24 | ; Electrostatics 25 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 26 | pme_order = 4 ; cubic interpolation 27 | fourierspacing = 0.16 ; grid spacing for FFT 28 | ; Temperature coupling is on 29 | tcoupl = Nose-Hoover ; More accurate thermostat 30 | tc-grps = Protein_DPPC Water_and_ions ; two coupling groups - more accurate 31 | tau_t = 0.5 0.5 ; time constant, in ps 32 | ref_t = 323 323 ; reference temperature, one for each group, in K 33 | ; Pressure coupling is on 34 | pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 35 | pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z 36 | tau_p = 2.0 ; time constant, in ps 37 | ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) 38 | compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 39 | ; Periodic boundary conditions 40 | pbc = xyz ; 3-D PBC 41 | ; Dispersion correction 42 | DispCorr = EnerPres ; account for cut-off vdW scheme 43 | ; Velocity generation 44 | gen_vel = no ; Velocity generation is off 45 | ; COM motion removal 46 | ; These options remove motion of the protein/bilayer relative to the solvent/ions 47 | nstcomm = 1 48 | comm-mode = Linear 49 | comm-grps = Protein_DPPC Water_and_ions 50 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/minim.mdp: -------------------------------------------------------------------------------- 1 | ; minim.mdp - used as input into grompp to generate em.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Energy step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | ns_type = grid ; Method to determine neighbor list (simple, grid) 11 | rlist = 1.2 ; Cut-off for making neighbor list (short range forces) 12 | coulombtype = PME ; Treatment of long range electrostatic interactions 13 | rcoulomb = 1.2 ; Short-range electrostatic cut-off 14 | rvdw = 1.2 ; Short-range Van der Waals cut-off 15 | pbc = xyz ; Periodic Boundary Conditions 16 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/minim_inflategro.mdp: -------------------------------------------------------------------------------- 1 | ; minim.mdp - used as input into grompp to generate em.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | define = -DSTRONG_POSRES ; Prevent protein from moving 4 | integrator = steep ; Algorithm (steep = steepest descent minimization) 5 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 6 | emstep = 0.01 ; Energy step size 7 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 8 | 9 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 10 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 11 | cutoff-scheme = Verlet ; Buffered neighbor searching 12 | ns_type = grid ; Method to determine neighbor list (simple, grid) 13 | rlist = 1.2 ; Cut-off for making neighbor list (short range forces) 14 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 15 | rcoulomb = 1.2 ; Short-range electrostatic cut-off 16 | rvdw = 1.2 ; Short-range Van der Waals cut-off 17 | pbc = xyz ; Periodic Boundary Conditions 18 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/npt.mdp: -------------------------------------------------------------------------------- 1 | title = NPT Equilibration for KALP15-DPPC 2 | define = -DPOSRES ; position restrain the protein 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstxout = 100 ; save coordinates every 0.2 ps 9 | nstvout = 100 ; save velocities every 0.2 ps 10 | nstenergy = 100 ; save energies every 0.2 ps 11 | nstlog = 100 ; update log file every 0.2 ps 12 | ; Bond parameters 13 | continuation = yes ; Restarting after NVT 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Neighborsearching 19 | ns_type = grid ; search neighboring grid cels 20 | nstlist = 5 ; 10 fs 21 | rlist = 1.2 ; short-range neighborlist cutoff (in nm) 22 | rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 24 | ; Electrostatics 25 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 26 | pme_order = 4 ; cubic interpolation 27 | fourierspacing = 0.16 ; grid spacing for FFT 28 | ; Temperature coupling is on 29 | tcoupl = Nose-Hoover ; More accurate thermostat 30 | tc-grps = Protein_DPPC Water_and_ions ; two coupling groups - more accurate 31 | tau_t = 0.5 0.5 ; time constant, in ps 32 | ref_t = 323 323 ; reference temperature, one for each group, in K 33 | ; Pressure coupling is on 34 | pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 35 | pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z 36 | tau_p = 5.0 ; time constant, in ps 37 | ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) 38 | compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 39 | ; Periodic boundary conditions 40 | pbc = xyz ; 3-D PBC 41 | ; Dispersion correction 42 | DispCorr = EnerPres ; account for cut-off vdW scheme 43 | ; Velocity generation 44 | gen_vel = no ; Velocity generation is off 45 | ; COM motion removal 46 | ; These options remove motion of the protein/bilayer relative to the solvent/ions 47 | nstcomm = 1 48 | comm-mode = Linear 49 | comm-grps = Protein_DPPC Water_and_ions 50 | ; Scale COM of reference coordinates 51 | refcoord_scaling = com 52 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/nvt.mdp: -------------------------------------------------------------------------------- 1 | title = NVT equilibration for KALP15-DPPC 2 | define = -DPOSRES ; position restrain the protein 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstxout = 100 ; save coordinates every 0.2 ps 9 | nstvout = 100 ; save velocities every 0.2 ps 10 | nstenergy = 100 ; save energies every 0.2 ps 11 | nstlog = 100 ; update log file every 0.2 ps 12 | ; Bond parameters 13 | continuation = no ; first dynamics run 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Neighborsearching 19 | ns_type = grid ; search neighboring grid cels 20 | nstlist = 5 ; 10 fs 21 | rlist = 1.2 ; short-range neighborlist cutoff (in nm) 22 | rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.2 ; short-range van der Waals cutoff (in nm) 24 | ; Electrostatics 25 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 26 | pme_order = 4 ; cubic interpolation 27 | fourierspacing = 0.16 ; grid spacing for FFT 28 | ; Temperature coupling is on 29 | tcoupl = V-rescale ; modified Berendsen thermostat 30 | tc-grps = Protein_DPPC Water_and_ions ; two coupling groups - more accurate 31 | tau_t = 0.1 0.1 ; time constant, in ps 32 | ref_t = 323 323 ; reference temperature, one for each group, in K 33 | ; Pressure coupling is off 34 | pcoupl = no ; no pressure coupling in NVT 35 | ; Periodic boundary conditions 36 | pbc = xyz ; 3-D PBC 37 | ; Dispersion correction 38 | DispCorr = EnerPres ; account for cut-off vdW scheme 39 | ; Velocity generation 40 | gen_vel = yes ; assign velocities from Maxwell distribution 41 | gen_temp = 323 ; temperature for Maxwell distribution 42 | gen_seed = -1 ; generate a random seed 43 | ; COM motion removal 44 | ; These options remove motion of the protein/bilayer relative to the solvent/ions 45 | nstcomm = 1 46 | comm-mode = Linear 47 | comm-grps = Protein_DPPC Water_and_ions 48 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/run_inflategro.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # This script assumes you have already inflated the system with the InflateGRO command 4 | # provided in the tutorial, and that you have further updated topol.top correctly to 5 | # reflect the number of DPPC lipids that were deleted. 6 | # 7 | # This script assumes that the gmx binary is in the $PATH and that all necessary input 8 | # files (coordinates, topology, .mdp) are in the current working directory. 9 | # 10 | # Confirm that you have achieved an appropriate area per lipid by inspecting the area_shrink*.dat 11 | # files along the shrinking iterations. 12 | 13 | # prevent accumulation of backup files like mdout.mdp 14 | export GMX_MAXBACKUP=-1 15 | 16 | # Run energy minimization on the inflated system 17 | gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr 18 | gmx mdrun -deffnm system_inflated_em 19 | 20 | # make molecules whole 21 | echo 0 | gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc mol 22 | mv tmp.gro system_inflated_em.gro 23 | 24 | # loop over 26 shrinking iterations 25 | for curr in {1..26} 26 | do 27 | echo "########################################" 28 | echo "#" 29 | echo "# RUNNING SHRINKING ITERATION ${curr}..." 30 | echo "#" 31 | echo "########################################" 32 | 33 | prev=$((curr - 1)) 34 | 35 | if [ $curr -eq 1 ]; then 36 | if [ ! -e system_inflated_em.gro ]; then 37 | echo "system_inflated_em.gro does not exist! Exiting." 38 | exit; 39 | fi 40 | # special file name if doing the first iteration 41 | perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0 system_shrink${curr}.gro 5 area_shrink${curr}.dat 42 | else 43 | if [ ! -e system_shrink${prev}_em.gro ]; then 44 | echo "system_shrink${prev}_em.gro does not exist! Exiting." 45 | exit; 46 | fi 47 | # otherwise use minimized coordinates from previous iteration 48 | perl inflategro.pl system_shrink${prev}_em.gro 0.95 DPPC 0 system_shrink${curr}.gro 5 area_shrink${curr}.dat 49 | fi 50 | 51 | # run grompp and mdrun to carry out energy minimization 52 | gmx grompp -f minim_inflategro.mdp -c system_shrink${curr}.gro -r system_shrink${curr}.gro -p topol.top -o system_shrink${curr}_em.tpr 53 | gmx mdrun -deffnm system_shrink${curr}_em 54 | 55 | # make molecules whole 56 | gmx trjconv -s system_shrink${curr}_em.tpr -f system_shrink${curr}_em.gro -o tmp.gro -pbc mol 57 | mv tmp.gro system_shrink${curr}_em.gro 58 | 59 | done 60 | 61 | exit; 62 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/topol_dppc.top: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'topol_dppc.top' was generated 3 | ; By user: jalemkul (502) 4 | ; On host: bevany.biochem.vt.edu 5 | ; At date: Fri Oct 20 13:26:53 2006 6 | ; 7 | ; This is your topology file 8 | ; 9 | ; Include chain topologies 10 | #include "gromos53a6_lipid.ff/forcefield.itp" 11 | #include "dppc.itp" 12 | 13 | ; Include water topology 14 | #include "gromos53a6_lipid.ff/spc.itp" 15 | 16 | ; Include ion topologies 17 | #include "gromos53a6_lipid.ff/ions.itp" 18 | 19 | ; System specifications 20 | [ system ] 21 | 128-Lipid DPPC Bilayer 22 | 23 | [ molecules ] 24 | ; molecule name nr. 25 | DPPC 128 26 | SOL 3655 27 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/topol_dppc_old.top: -------------------------------------------------------------------------------- 1 | ; 2 | ; File 'A_128.top' was generated 3 | ; By user: jalemkul (502) 4 | ; On host: bevany.biochem.vt.edu 5 | ; At date: Fri Oct 20 13:26:53 2006 6 | ; 7 | ; This is your topology file 8 | ; 1SOL OW 1 -2.449 -4.190 -1.80 9 | ; 10 | ; Include chain topologies 11 | #include "ffG53a6_lipid.itp" 12 | #include "dppc.itp" 13 | 14 | ; Include water topology 15 | #include "spc.itp" 16 | 17 | ; Include ion topologies 18 | #include "ions.itp" 19 | 20 | ; System specifications 21 | [ system ] 22 | 128-Lipid DPPC Bilayer 23 | 24 | [ molecules ] 25 | ; molecule name nr. 26 | DPPC 128 27 | SOL 3655 28 | -------------------------------------------------------------------------------- /tutorial-files/membrane_protein/water_deletor.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | 5 | # Written by Justin Lemkul, Ph.D. 6 | # Contact: jalemkul@vt.edu 7 | # 6/7/2017 8 | # 9 | # License: GPL-3.0 or later, at user's option 10 | 11 | # This script deletes out waters between certain z-coordinate values 12 | # Z-values are specified by a chosen atom on the command line 13 | # The decision on how to split "top" of bilayer from "bottom" - define "middle" atom, 14 | # is taken from the command line. If z(reference) > z(middle) -> top, and vice versa 15 | # Determine average z-coordinate value for top and bottom, if OW of water falls within 16 | # that range, delete it and its corresponding HW's 17 | 18 | # Collect stuff from command line arguments into a hash 19 | unless (@ARGV) 20 | { 21 | die "Example usage: perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref O33 -middle C50 -water 3 -v [yes/no]\n"; 22 | } 23 | 24 | print "\nStarting water deletion process...\n"; 25 | 26 | my %args = @ARGV; 27 | my $input; 28 | my $output; 29 | my $ref_atom; 30 | my $middle_atom; 31 | my $nwater; 32 | my $verbose; 33 | 34 | if (exists($args{"-in"})) 35 | { 36 | $input = $args{"-in"}; 37 | } 38 | else 39 | { 40 | die "No input specified!\n"; 41 | } 42 | 43 | # collect all the input lines into an array 44 | open(IN, $input); 45 | my @in = ; 46 | close(IN); 47 | 48 | # grab some stuff from the input (non-atom lines) 49 | my $header = shift(@in); 50 | my $orig_natoms = shift(@in); 51 | chomp($orig_natoms); 52 | my $box = pop(@in); 53 | 54 | if (exists($args{"-out"})) 55 | { 56 | $output = $args{"-out"}; 57 | } 58 | else 59 | { 60 | print "Using default output filename of \"bilayer_fix.gro\"\n"; 61 | $output = "bilayer_fix.gro"; 62 | } 63 | 64 | if (exists($args{"-ref"})) 65 | { 66 | $ref_atom = $args{"-ref"}; 67 | } 68 | else 69 | { 70 | die "No reference atom specified!\n"; 71 | } 72 | 73 | if (exists($args{"-middle"})) 74 | { 75 | $middle_atom = $args{"-middle"}; 76 | } 77 | else 78 | { 79 | die "No middle atom specified!\n"; 80 | } 81 | 82 | # define number of water atoms for splicing 83 | if (exists($args{"-water"})) 84 | { 85 | $nwater = $args{"-water"}; 86 | } 87 | else 88 | { 89 | print "Option -nwater not set, assuming 3 atoms in the water model.\n"; 90 | $nwater = 3; 91 | } 92 | 93 | # define verbosity 94 | if (exists($args{"-v"}) && (($args{"-v"} eq "yes") || ($args{"-v"} eq "Yes") || ($args{"-v"} eq "y") || ($args{"-v"} eq "Y"))) 95 | { 96 | $verbose = 1; 97 | } 98 | else 99 | { 100 | $verbose = 0; # default to non-verbose mode 101 | } 102 | 103 | # process input file to strip out all lines corresponding to reference or middle atoms 104 | my @ref_atoms; 105 | my @middle_atoms; 106 | 107 | # also count how many water molecules we start with 108 | my $nwater_start = 0; 109 | 110 | foreach $_ (@in) 111 | { 112 | my @data = split(" ", $_); 113 | my $atom = $data[1]; 114 | 115 | if ($atom =~ /$ref_atom/) 116 | { 117 | push(@ref_atoms, $_); 118 | } 119 | elsif ($atom =~ /$middle_atom/) 120 | { 121 | push(@middle_atoms, $_); 122 | } 123 | elsif ($atom =~ /OW/) 124 | { 125 | $nwater_start++; 126 | } 127 | } 128 | 129 | # determine the middle of the bilayer from the middle atoms 130 | # middle of bilayer is defined as the average z-coordinate of the middle atoms 131 | my $total_z; 132 | my $nmiddle = scalar(@middle_atoms); 133 | 134 | foreach $_ (@middle_atoms) 135 | { 136 | my @data = split(" ", $_); 137 | my $z = 0; 138 | # last field on line if no velocities, otherwise n-3 139 | if (scalar(@data) > 6) 140 | { 141 | # there are velocities 142 | $z = $data[scalar(@data)-4]; 143 | } 144 | else 145 | { 146 | $z = $data[scalar(@data)-1]; 147 | } 148 | # debug 149 | #print "$z\n"; 150 | 151 | $total_z += $z; 152 | } 153 | 154 | my $middle_z = $total_z / $nmiddle; 155 | 156 | print "Defining the middle of the bilayer as z = $middle_z.\n"; 157 | 158 | # now split the reference atoms into top and bottom 159 | my @top_ref; 160 | my @bottom_ref; 161 | 162 | foreach $_ (@ref_atoms) 163 | { 164 | my @data = split(" ", $_); 165 | my $z = 0; 166 | # last field on line if no velocities, otherwise n-3 167 | if (scalar(@data) > 6) 168 | { 169 | # there are velocities 170 | $z = $data[scalar(@data)-4]; 171 | } 172 | else 173 | { 174 | $z = $data[scalar(@data)-1]; 175 | } 176 | 177 | if ($z > $middle_z) 178 | { 179 | push(@top_ref, $_); 180 | } 181 | elsif ($z < $middle_z) 182 | { 183 | push(@bottom_ref, $_); 184 | } 185 | else 186 | { 187 | print "Weird z-coordinate found!\n"; 188 | print "$_\n"; 189 | } 190 | } 191 | 192 | # determine average z-coordinate values for the top and bottom reference atoms 193 | my $top_z; 194 | my $ntop = scalar(@top_ref); 195 | 196 | # debug 197 | print "ntop = $ntop\n"; 198 | 199 | foreach $_ (@top_ref) 200 | { 201 | my @data = split(" ", $_); 202 | my $z = 0; 203 | # last field on line if no velocities, otherwise n-3 204 | if (scalar(@data) > 6) 205 | { 206 | # there are velocities 207 | $z = $data[scalar(@data)-4]; 208 | } 209 | else 210 | { 211 | $z = $data[scalar(@data)-1]; 212 | } 213 | # debug 214 | print "$z\n"; 215 | 216 | $top_z += $z; 217 | } 218 | 219 | my $top_z_avg = $top_z / $ntop; 220 | 221 | my $bottom_z; 222 | my $nbottom = scalar(@bottom_ref); 223 | 224 | foreach $_ (@bottom_ref) 225 | { 226 | my @data = split(" ", $_); 227 | my $z = 0; 228 | # last field on line if no velocities, otherwise n-3 229 | if (scalar(@data) > 6) 230 | { 231 | # there are velocities 232 | $z = $data[scalar(@data)-4]; 233 | } 234 | else 235 | { 236 | $z = $data[scalar(@data)-1]; 237 | } 238 | 239 | $bottom_z += $z; 240 | } 241 | 242 | my $bottom_z_avg = $bottom_z / $nbottom; 243 | 244 | print "Boundaries for eliminating water are $bottom_z_avg < z < $top_z_avg.\n"; 245 | 246 | # now actually delete the waters 247 | # go thru the input file and find any OW that has a z-coordinate within the bounds 248 | # defined above. 249 | my @clean_atoms; 250 | 251 | my $size = scalar(@in); 252 | 253 | my $ndel = 0; # keep track of how many waters we have deleted 254 | 255 | for (my $i=0; $i<$size; $i++) 256 | { 257 | my @line = split(" ", $in[$i]); 258 | # account for the fact that at high atom numbers, the string is joined, i.e. OW10000 259 | my $atom = substr($line[1], 0, 2); 260 | # get last entry - in the above case, OW10000, there is no distinct atom number 261 | my $z = $line[(scalar(@line)-1)]; 262 | 263 | unless ($atom eq "OW") 264 | { 265 | push(@clean_atoms, $in[$i]); 266 | } 267 | else 268 | { 269 | if (($z > $bottom_z_avg) && ($z < $top_z_avg)) 270 | { 271 | # assemble the residue numbering for printing/bookkeeping 272 | if ($verbose == 1) 273 | { 274 | my @res = split('', $line[0]); 275 | pop(@res); # get rid of "SOL" 276 | pop(@res); 277 | pop(@res); 278 | my $resnr = join('', @res); 279 | print "Deleting residue $resnr\n"; 280 | } 281 | 282 | # debug 283 | # my @delete = splice(@in, $i, 3); 284 | # print "@delete"; 285 | 286 | splice(@in, $i, $nwater); 287 | $i--; 288 | $size -= $nwater; 289 | $ndel++; 290 | } 291 | else 292 | { 293 | push(@clean_atoms, $in[$i]); 294 | } 295 | } 296 | } 297 | 298 | # Report what happened 299 | print "$ndel water molecules have been deleted.\n"; 300 | my $watnew = $nwater_start - $ndel; 301 | print "$watnew water molecules remain. Update your topology!\n"; 302 | 303 | # print the cleaned output 304 | my $natoms_clean = scalar(@clean_atoms); 305 | 306 | open(OUT, ">$output"); 307 | print OUT $header; 308 | print OUT "$natoms_clean\n"; 309 | 310 | foreach $_ (@clean_atoms) 311 | { 312 | print OUT "$_"; 313 | } 314 | 315 | print OUT $box; 316 | 317 | close(OUT); 318 | 319 | print "\nOutput file $output written. You may want to renumber the file with,\n"; 320 | print "for example, genconf in the GROMACS package.\n\n"; 321 | 322 | exit; 323 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/get_distances.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | ################################################# 4 | # get_distances.sh 5 | # 6 | # Script iteratively calls gmx distance and 7 | # assembles a series of COM distance values 8 | # indexed by frame number, for use in 9 | # preparing umbrella sampling windows. 10 | # 11 | # Written by: Justin A. Lemkul, Ph.D. 12 | # Contact: jalemkul@vt.edu 13 | # 14 | ################################################# 15 | 16 | echo 0 | gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep 17 | 18 | # compute distances 19 | for (( i=0; i<501; i++ )) 20 | do 21 | gmx distance -s pull.tpr -f conf${i}.gro -n index.ndx -select 'com of group "Chain_A" plus com of group "Chain_B"' -oall dist${i}.xvg 22 | done 23 | 24 | # compile summary 25 | touch summary_distances.dat 26 | for (( i=0; i<501; i++ )) 27 | do 28 | d=`tail -n 1 dist${i}.xvg | awk '{print $2}'` 29 | echo "${i} ${d}" >> summary_distances.dat 30 | rm dist${i}.xvg 31 | done 32 | 33 | exit; 34 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/ions.mdp: -------------------------------------------------------------------------------- 1 | ; ions.mdp - used as input into grompp to generate ions.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Energy step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | cutoff-scheme = Verlet ; Buffered neighbor searching 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | rlist = 1.4 ; Cut-off for making neighbor list (short range forces) 13 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 14 | rcoulomb = 1.4 ; Short-range electrostatic cut-off 15 | rvdw = 1.4 ; Short-range Van der Waals cut-off 16 | pbc = xyz ; Periodic Boundary Conditions 17 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/md_pull.mdp: -------------------------------------------------------------------------------- 1 | title = Umbrella pulling simulation 2 | define = -DPOSRES_B 3 | ; Run parameters 4 | integrator = md 5 | dt = 0.002 6 | tinit = 0 7 | nsteps = 250000 ; 500 ps 8 | nstcomm = 10 9 | ; Output parameters 10 | nstxout = 5000 ; every 10 ps 11 | nstvout = 5000 12 | nstfout = 500 13 | nstxtcout = 500 ; every 1 ps 14 | nstenergy = 500 15 | ; Bond parameters 16 | constraint_algorithm = lincs 17 | constraints = all-bonds 18 | continuation = yes ; continuing from NPT 19 | ; Single-range cutoff scheme 20 | cutoff-scheme = Verlet 21 | nstlist = 20 22 | ns_type = grid 23 | rlist = 1.4 24 | rcoulomb = 1.4 25 | rvdw = 1.4 26 | ; PME electrostatics parameters 27 | coulombtype = PME 28 | fourierspacing = 0.12 29 | fourier_nx = 0 30 | fourier_ny = 0 31 | fourier_nz = 0 32 | pme_order = 4 33 | ewald_rtol = 1e-5 34 | optimize_fft = yes 35 | ; Berendsen temperature coupling is on in two groups 36 | Tcoupl = Nose-Hoover 37 | tc_grps = Protein Non-Protein 38 | tau_t = 1.0 1.0 39 | ref_t = 310 310 40 | ; Pressure coupling is on 41 | Pcoupl = Parrinello-Rahman 42 | pcoupltype = isotropic 43 | tau_p = 1.0 44 | compressibility = 4.5e-5 45 | ref_p = 1.0 46 | refcoord_scaling = com 47 | ; Generate velocities is off 48 | gen_vel = no 49 | ; Periodic boundary conditions are on in all directions 50 | pbc = xyz 51 | ; Long-range dispersion correction 52 | DispCorr = EnerPres 53 | ; Pull code 54 | pull = yes 55 | pull_ncoords = 1 ; only one reaction coordinate 56 | pull_ngroups = 2 ; two groups defining one reaction coordinate 57 | pull_group1_name = Chain_A 58 | pull_group2_name = Chain_B 59 | pull_coord1_type = umbrella ; harmonic potential 60 | pull_coord1_geometry = distance ; simple distance increase 61 | pull_coord1_dim = N N Y 62 | pull_coord1_groups = 1 2 63 | pull_coord1_start = yes ; define initial COM distance > 0 64 | pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns 65 | pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 66 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/md_umbrella.mdp: -------------------------------------------------------------------------------- 1 | title = Umbrella pulling simulation 2 | define = -DPOSRES_B 3 | ; Run parameters 4 | integrator = md 5 | dt = 0.002 6 | tinit = 0 7 | nsteps = 5000000 ; 10 ns 8 | nstcomm = 10 9 | ; Output parameters 10 | nstxout-compressed = 5000 ; every 10 ps 11 | nstenergy = 5000 12 | ; Bond parameters 13 | constraint_algorithm = lincs 14 | constraints = all-bonds 15 | continuation = yes 16 | ; Single-range cutoff scheme 17 | cutoff-scheme = Verlet 18 | nstlist = 20 19 | ns_type = grid 20 | rlist = 1.4 21 | rcoulomb = 1.4 22 | rvdw = 1.4 23 | ; PME electrostatics parameters 24 | coulombtype = PME 25 | fourierspacing = 0.12 26 | fourier_nx = 0 27 | fourier_ny = 0 28 | fourier_nz = 0 29 | pme_order = 4 30 | ewald_rtol = 1e-5 31 | optimize_fft = yes 32 | ; Berendsen temperature coupling is on in two groups 33 | Tcoupl = Nose-Hoover 34 | tc_grps = Protein Non-Protein 35 | tau_t = 1.0 1.0 36 | ref_t = 310 310 37 | ; Pressure coupling is on 38 | Pcoupl = Parrinello-Rahman 39 | pcoupltype = isotropic 40 | tau_p = 1.0 41 | compressibility = 4.5e-5 42 | ref_p = 1.0 43 | refcoord_scaling = com 44 | ; Generate velocities is off 45 | gen_vel = no 46 | ; Periodic boundary conditions are on in all directions 47 | pbc = xyz 48 | ; Long-range dispersion correction 49 | DispCorr = EnerPres 50 | ; Pull code 51 | pull = yes 52 | pull_ncoords = 1 ; only one reaction coordinate 53 | pull_ngroups = 2 ; two groups defining one reaction coordinate 54 | pull_group1_name = Chain_A 55 | pull_group2_name = Chain_B 56 | pull_coord1_type = umbrella ; harmonic potential 57 | pull_coord1_geometry = distance ; simple distance increase 58 | pull_coord1_dim = N N Y 59 | pull_coord1_groups = 1 2 60 | pull_coord1_start = yes ; define initial COM distance > 0 61 | pull_coord1_rate = 0.0 ; restrain in place 62 | pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 63 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/minim.mdp: -------------------------------------------------------------------------------- 1 | ; ions.mdp - used as input into grompp to generate ions.tpr 2 | ; Parameters describing what to do, when to stop and what to save 3 | integrator = steep ; Algorithm (steep = steepest descent minimization) 4 | emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 5 | emstep = 0.01 ; Energy step size 6 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 7 | 8 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 9 | nstlist = 1 ; Frequency to update the neighbor list and long range forces 10 | cutoff-scheme = Verlet ; Buffered neighbor searching 11 | ns_type = grid ; Method to determine neighbor list (simple, grid) 12 | rlist = 1.4 ; Cut-off for making neighbor list (short range forces) 13 | coulombtype = PME ; Treatment of long range electrostatic interactions 14 | rcoulomb = 1.4 ; Short-range electrostatic cut-off 15 | rvdw = 1.4 ; Short-range Van der Waals cut-off 16 | pbc = xyz ; Periodic Boundary Conditions 17 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/npt.mdp: -------------------------------------------------------------------------------- 1 | title = NPT Equilibration 2 | define = -DPOSRES ; position restrain the protein 3 | ; Run parameters 4 | integrator = md ; leap-frog integrator 5 | nsteps = 50000 ; 2 * 50000 = 100 ps 6 | dt = 0.002 ; 2 fs 7 | ; Output control 8 | nstxout = 1000 ; save coordinates every 2 ps 9 | nstvout = 1000 ; save velocities every 2 ps 10 | nstenergy = 1000 ; save energies every 2 ps 11 | nstlog = 1000 ; update log file every 2 ps 12 | ; Bond parameters 13 | continuation = no ; Initial simulation 14 | constraint_algorithm = lincs ; holonomic constraints 15 | constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 16 | lincs_iter = 1 ; accuracy of LINCS 17 | lincs_order = 4 ; also related to accuracy 18 | ; Neighborsearching 19 | ns_type = grid ; search neighboring grid cels 20 | nstlist = 5 ; 10 fs 21 | rlist = 1.4 ; short-range neighborlist cutoff (in nm) 22 | rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) 23 | rvdw = 1.4 ; short-range van der Waals cutoff (in nm) 24 | ; Electrostatics 25 | coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 26 | pme_order = 4 ; cubic interpolation 27 | fourierspacing = 0.16 ; grid spacing for FFT 28 | ; Temperature coupling is on 29 | tcoupl = Berendsen ; Weak coupling for initial equilibration 30 | tc-grps = Protein Non-Protein ; two coupling groups - more accurate 31 | tau_t = 0.1 0.1 ; time constant, in ps 32 | ref_t = 310 310 ; reference temperature, one for each group, in K 33 | ; Pressure coupling is on 34 | pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling 35 | pcoupltype = isotropic ; uniform scaling of x-y-z box vectors 36 | tau_p = 2.0 ; time constant, in ps 37 | ref_p = 1.0 ; reference pressure (in bar) 38 | compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 39 | refcoord_scaling = com 40 | ; Periodic boundary conditions 41 | pbc = xyz ; 3-D PBC 42 | ; Dispersion correction 43 | DispCorr = EnerPres ; account for cut-off vdW scheme 44 | ; Velocity generation 45 | gen_vel = yes ; Velocity generation is on 46 | gen_temp = 310 ; temperature for velocity generation 47 | gen_seed = -1 ; random seed 48 | ; COM motion removal 49 | ; These options remove COM motion of the system 50 | nstcomm = 10 51 | comm-mode = Linear 52 | comm-grps = System 53 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/npt_umbrella.mdp: -------------------------------------------------------------------------------- 1 | title = Umbrella pulling simulation 2 | define = -DPOSRES_B 3 | ; Run parameters 4 | integrator = md 5 | dt = 0.002 6 | tinit = 0 7 | nsteps = 50000 ; 100 ps 8 | nstcomm = 10 9 | ; Output parameters 10 | nstvout = 5000 ; every 10 ps 11 | nstfout = 5000 12 | nstxout-compressed = 5000 13 | nstenergy = 5000 14 | ; Bond parameters 15 | constraint_algorithm = lincs 16 | constraints = all-bonds 17 | continuation = no 18 | ; Single-range cutoff scheme 19 | cutoff-scheme = Verlet 20 | nstlist = 20 21 | ns_type = grid 22 | rlist = 1.4 23 | rcoulomb = 1.4 24 | rvdw = 1.4 25 | ; PME electrostatics parameters 26 | coulombtype = PME 27 | fourierspacing = 0.12 28 | fourier_nx = 0 29 | fourier_ny = 0 30 | fourier_nz = 0 31 | pme_order = 4 32 | ewald_rtol = 1e-5 33 | optimize_fft = yes 34 | ; Berendsen temperature coupling is on in two groups 35 | Tcoupl = Berendsen 36 | tc_grps = Protein Non-Protein 37 | tau_t = 0.5 0.5 38 | ref_t = 310 310 39 | ; Pressure coupling is on 40 | Pcoupl = Berendsen 41 | pcoupltype = isotropic 42 | tau_p = 1.0 43 | compressibility = 4.5e-5 44 | ref_p = 1.0 45 | refcoord_scaling = com 46 | ; Generate velocities is on 47 | gen_vel = yes 48 | gen_temp = 310 49 | ; Periodic boundary conditions are on in all directions 50 | pbc = xyz 51 | ; Long-range dispersion correction 52 | DispCorr = EnerPres 53 | ; Pull code 54 | pull = yes 55 | pull_ncoords = 1 ; only one reaction coordinate 56 | pull_ngroups = 2 ; two groups defining one reaction coordinate 57 | pull_group1_name = Chain_A 58 | pull_group2_name = Chain_B 59 | pull_coord1_type = umbrella ; harmonic potential 60 | pull_coord1_geometry = distance ; simple distance increase 61 | pull_coord1_dim = N N Y 62 | pull_coord1_groups = 1 2 63 | pull_coord1_start = yes ; define initial COM distance > 0 64 | pull_coord1_rate = 0.0 ; restrain in place 65 | pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 66 | -------------------------------------------------------------------------------- /tutorial-files/umbrella/setup-umbrella-script.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jalemkul/gmx_tutorials_livecoms/b0778734673300ee6c34f04aa0cc5fac4bc32f3d/tutorial-files/umbrella/setup-umbrella-script.tar.gz -------------------------------------------------------------------------------- /tutorial-files/vsites/co2.pdb: -------------------------------------------------------------------------------- 1 | TITLE CO2 with dummy masses 2 | REMARK THIS IS A SIMULATION BOX 3 | CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 4 | MODEL 1 5 | ATOM 1 O1 CO2 1 0.000 0.000 0.000 1.00 0.00 6 | ATOM 2 C CO2 1 1.250 0.000 0.000 1.00 0.00 7 | ATOM 3 O2 CO2 1 2.500 0.000 0.000 1.00 0.00 8 | ATOM 4 M1 CO2 1 0.180 0.000 0.000 1.00 0.00 9 | ATOM 5 M2 CO2 1 2.320 0.000 0.000 1.00 0.00 10 | TER 11 | ENDMDL 12 | -------------------------------------------------------------------------------- /tutorial-files/vsites/em.mdp: -------------------------------------------------------------------------------- 1 | ; Parameters describing what to do, when to stop and what to save 2 | integrator = steep ; Algorithm (steep = steepest descent minimization) 3 | emtol = 10.0 ; Stop minimization when the maximum force < 10.0 kJ/mol 4 | emstep = 0.01 ; Energy step size 5 | nsteps = 50000 ; Maximum number of (minimization) steps to perform 6 | 7 | ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 8 | cutoff-scheme = group 9 | nstlist = 0 ; Frequency to update the neighbor list and long range forces 10 | ns_type = simple ; Method to determine neighbor list (simple, grid) 11 | rlist = 0 ; Cut-off for making neighbor list (short range forces) 12 | coulombtype = cutoff ; Treatment of long range electrostatic interactions 13 | rcoulomb = 0 ; long range electrostatic cut-off 14 | rvdw = 0 ; long range van der Waals cut-off 15 | pbc = no ; no PBC to model gas phase 16 | -------------------------------------------------------------------------------- /tutorial-files/vsites/md.mdp: -------------------------------------------------------------------------------- 1 | ; Parameters describing what to do, when to stop and what to save 2 | integrator = md ; leap-frog integrator 3 | nsteps = 50000 ; Maximum number of steps to perform 4 | dt = 0.002 ; 2 fs * 50000 steps = 100 ps 5 | 6 | ; output 7 | nstxout = 500 8 | 9 | ; temperature coupling 10 | tcoupl = V-rescale 11 | tc_grps = System 12 | tau_t = 0.1 13 | ref_t = 298 14 | 15 | gen_vel = yes 16 | gen_temp = 298 17 | gen_seed = -1 18 | 19 | ; Settings below are for the all-vs-all kernels 20 | cutoff-scheme = group 21 | nstlist = 0 ; Fixed neighbor list 22 | ns_type = simple ; Method to determine neighbor list (simple, grid) 23 | coulombtype = cutoff ; Infinite cutoffs used here 24 | rlist = 0 25 | rcoulomb = 0 ; short range electrostatic cut-off (0 = infinite) 26 | rvdw = 0 ; short range van der Waals cut-off (0 = infinite) 27 | pbc = no ; Non-periodic system 28 | comm-mode = angular 29 | -------------------------------------------------------------------------------- /tutorial-files/vsites/topol.top: -------------------------------------------------------------------------------- 1 | ; CO2 topology with virtual sites 2 | ; 3 | ; Two massive particles that each have 1/2 the mass of CO2 4 | ; Each massive particle has no nonbonded interactions 5 | ; The virtual sites represent C and O atoms, which have charge 6 | ; and LJ parameters but no mass 7 | ; 8 | ; Overall structure is O--M---C---M--O where "M" indicate mass centers 9 | ; 10 | ; Moment of inertia and total mass must be correct 11 | ; Mass is easy - each mass center is 1/2 * mass(CO2) 12 | ; 13 | ; Total mass = (2 * 15.9994) + 12.011 = 44.0098 amu 14 | ; each M particle has a mass of 22.0049 amu 15 | ; 16 | ; Moment of inertia for three linear atoms 17 | ; I = 2 * m_O * L^2 18 | ; where L is the C=O bond length 19 | ; 20 | ; I = 2 * (15.9994) * (0.125)^2 21 | ; I = 31.9988 * 0.015625 22 | ; I = 0.49998125 23 | ; 24 | ; Moment of inertia for two atoms 25 | ; I = ((m_A * m_B)/m_Total) * L^2 26 | ; L = sqrt[ I/((m_A * m_B)/m_Total) ] 27 | ; L = sqrt[ 0.49998125 / ((22.0049 * 22.0049)/44.0098) 28 | ; L = sqrt[ 0.49998125 / 11.00245 ] 29 | ; L = 0.213172980408142 30 | ; L = 0.213173 31 | ; 32 | ; L/2 = 0.10658649020407 33 | ; L/2 = 0.1065865 34 | ; 35 | ; 36 | ; PLEASE NOTE 37 | ; The charges on C and O atoms were taken from: 38 | ; Q. Yang and C. Zhong (2006) J. Phys. Chem. B 110: 17776-17783 39 | ; doi: 10.1021/jp062723w 40 | ; The validity of these charges within the OPLS-AA force field is not explicitly 41 | ; endorsed by their use here. As the purpose of this topology is to illustrate the 42 | ; use of virtual sites to create the model, these values are used for educational 43 | ; purposes only to produce a reasonably sensible topology. 44 | 45 | #include "oplsaa.ff/forcefield.itp" 46 | 47 | ; Here we introduce a special atom type to be used for each mass center 48 | [ atomtypes ] 49 | ; name bond_type mass charge ptype sigma epsilon 50 | MCO MCO 0.000 0.000 A 0.000 0.000 51 | 52 | [ moleculetype ] 53 | ; name nrexcl 54 | CO2 2 55 | 56 | [ atoms ] 57 | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 58 | 1 opls_272 1 CO2 O1 1 -0.350 0.0000 59 | 2 opls_271 1 CO2 C 1 0.700 0.0000 60 | 3 opls_272 1 CO2 O2 1 -0.350 0.0000 61 | 4 MCO 1 CO2 M1 1 0.000 22.0049 62 | 5 MCO 1 CO2 M2 1 0.000 22.0049 63 | 64 | [ constraints ] 65 | ; There are no bonds in this system 66 | ; Instead, we fix the distance between the mass centers such that 67 | ; the virtual sites can be reconstructed 68 | 4 5 1 0.213173 69 | 70 | [ virtual_sites2 ] 71 | ; the M--O distance is 0.125 - 0.1065865 = 0.0184135 72 | ; the M--M distance is 0.213173 73 | ; therefore, the fraction of the distance along the M--M length is (0.213173+0.0184135)/0.213173 = 1.0851116 74 | ; thus placing the virtual O sites beyond the M--M distance 75 | ; site ai aj funct a 76 | 1 4 5 1 1.0851116 ; relative to mass center 4, extends beyond mass center 5 77 | 2 4 5 1 0.5000 ; right in the middle 78 | 3 5 4 1 1.0851116 ; as in the case of site 1 79 | 80 | [ system ] 81 | CO2 in vacuo 82 | 83 | [ molecules ] 84 | CO2 1 85 | --------------------------------------------------------------------------------