├── 1_gromacs_install.pdf ├── 2_PDB_forcefield.pdf ├── 3_Protein_MD.pdf ├── 4_MD-Analysis.pdf ├── 5_Protein_ligand_Complex_MD.pdf ├── 6_GBSA.pdf ├── 7_charmm-gui_MemProtein.pdf ├── 8_Amber_MD.pdf ├── 9_Boltzmann_Distribution.pdf ├── Docker_files └── amber24 │ ├── Dockerfile │ └── run_cmake ├── MemMD_code ├── inputpdbs │ ├── 4236.pdb │ └── 4415.pdb ├── mdps │ ├── em.mdp │ ├── ions.mdp │ ├── md.mdp │ ├── npt.mdp │ ├── nvt.mdp │ ├── run_md.sh │ └── water_deletor.py ├── membrane │ ├── CL.itp │ ├── NA.itp │ ├── POPC.itp │ ├── POPC_posre.itp │ ├── TIP3P.itp │ ├── amber99sb-ildn_slipids.ff │ │ ├── Joung_et_al_ion_parameters.pdf │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── aminoacids.vsd │ │ ├── atomtypes.atp │ │ ├── dna.arn │ │ ├── dna.hdb │ │ ├── dna.r2b │ │ ├── dna.rtp.back │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gbsa.itp │ │ ├── ions.itp │ │ ├── rna.arn │ │ ├── rna.hdb │ │ ├── rna.r2b │ │ ├── rna.rtp.back │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ ├── urea.itp │ │ └── watermodels.dat │ ├── final-system-dry.pdb │ ├── protein_0.itp │ ├── protein_0_posre.itp │ └── topol_final_dry.top ├── mutiple_MD_3090.ipynb ├── mutiple_MD_3090.py └── readme ├── README.md ├── example_traj ├── index.ndx ├── md.gro ├── md.tpr └── md.xtc ├── maestro2amber.py ├── mdps ├── protein_MD │ ├── em.mdp │ ├── ions.mdp │ ├── md.mdp │ ├── npt.mdp │ └── nvt.mdp └── protein_ligand_complex_MD │ ├── em.mdp │ ├── ions.mdp │ ├── md.mdp │ ├── npt.mdp │ └── nvt.mdp └── plot ├── Dec.csv ├── plot_Dec.ipynb ├── plot_rmsd.ipynb ├── residue_total_energy.png ├── rmsd.xvg └── rmsd_plot.png /1_gromacs_install.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Sept-naf/gromacs-tutorials/HEAD/1_gromacs_install.pdf 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