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Molecular Dynamic with GROMACS

About Files in GROMACS

Protocol of GROMACS

Normal Protein MD

The tutorial gives Lysozyme as an example. First download the pdb file(PDB ID: 1AKI) from https://www.rcsb.org/: 

wget http://www.rcsb.org/pdb/files/1AKI.pdb
Delete water: 
grep -v HOH 1AKI.pdb > 1AKI_clean.pdb

Use pdb2gmx generate topological files

pdb2gmx is a tool to generate topological files GROMACS needs. In version 5.x, pbd2gmx is sub-unit of gmx command. pdb2gmx will generate 3 files:

  1. Topology file for the molecule.(.top)
  2. Position-restrained file.(.itp)
  3. Preprocessed structure file.(.gro)

gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
Parameters: -f:Input file -ff: Choose type of Force-Field, if don't choose ff type in command, gmx will list the ff type and will choose ff tyoe with index gmx provide, like below: 
Select the Force Field:
From current directory:
 1: CHARMM36 all-atom force field (July 2017)
From '/usr/local/gromacs/share/gromacs/top':
 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
-water:Choose the type of water model -o:Point the output file -ignh:Ignore hydrogen atoms

Defining Crystal Cells & Adding Solvents

Use editconf to define the box

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic
Parameters: -c:Put the protein in the center of the box -bt:Define the shape of Simulation box, cubic defines the cubic shape, dodecahedrondefines the dodecahedron box -d:Defines the edge of the box. Extend 1.0 nm at the maximum value in the coordinate direction

Add solvent with solvate
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

Add Ions with genion

To add ions into he system, we should first generate .tpr topology file with grompp. grompp uses .gro file and .top file ti generate topology file in atomic level. In this step, we need ions.mdp file. mdp file is like the profile(.conf) in NAMD. 

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
Then pass the trp file to genion and generate the ions. 
gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Run Energe-minimization, NVT and NPT

Energe Minimization

Generate em.trp: 

gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
Run MD: 
gmx mdrun -v -deffnm em
Parameters: -v:Print out every steps to the screen -deffnm；Defines the output file name

NVT
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr 
gmx mdrun -deffnm nvt
NPT
gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr 
gmx mdrun -deffnm npt

Run Product

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
gmx mdrun -deffnm md_0_1

Protein-Ligand

.MDP File and Adjusting Parameters