Download the structure from the Protein Data Bank (PDB): In this case we're using 2muj.pdb, a Plasmodium falciparum peptide.
First step: Initial configuration and topology, adding Hydrogens using pdb2gmx.
gmx_mpi pdb2gmx -f 2muj.pdb -o 2muj_H.pdb -ignh
select CHARMM36m force field and tip3p water model.
Second step: Building the box with PACKMOL. The peptide has 41 Angstroms size, so we're going to define 15 Angstroms for each side of the box: 41+15=56 Angstroms approximately.
./solvate.tcl 2muj_H.pdb -shell 15. -charge -1 -density 1.0 -o solvated.pdb
paste into packmol input file:
filetype pdb
seed -1
add_box_sides 1.0
output solvated.pdb
and run:
packmol < packmol_input.inp
Put the solvent and ion number in the end of the topology file (check the names in each force field). E.g.:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm36-jul2021.ff/ions.itp"
[ system ]
; Name
SERINE-REPEAT ANTIGEN PROTEIN
[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 4903
SOD 14
CLA 13
Third step: Build mdp files for each force field and run minimization.
gmx_mpi grompp -f mim.mdp -c solvated.pdb -r solvated.pdb -p topol.top -o minim.tpr -pp processed.top -maxwarn 1
gmx_mpi mdrun -v -deffnm minim
Fourth step: Run equilibration and choose ensembles.
NVT equilibration
gmx_mpi grompp -f nvt.mdp -c minim.gro -r minim.gro -p topol.top -o nvt.tpr
gmx_mpi mdrun -deffnm npt
NPT equilibration
gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -p topol.top -o npt.tpr
gmx_mpi mdrun -deffnm npt
Fifth step: MD production
gmx_mpi grompp -f md.mdp -c npt.gro -p topol.top -o md.tpr
gmx_mpi mdrun -deffnm md
GROMACS reminds you: "Creativity in science, as in art, cannot be organized. It arises spontaneously from individual talent. Well-run laboratories can foster it, but hierarchical organizations, inflexible bureaucratic rules, and mountains of futile paperwork can kill it." (Max Perutz)
(for now)