GROMACS

GPU build of GROMACS 2023.2 with common force fields available in the image.

For a more in-depth introduction to GROMACS for protein design, see our blog post.

Usage

One command per line; blank lines and # comments are ignored.
Commands must start with gmx/gmx_mpi or a bare subcommand (pdb2gmx, grompp, mdrun, trjconv, editconf, genion, solvate, make_ndx, genrestr, eneconv, genconf, x2top, dump, rms).
No pipes, &&, output redirects (>), or subshells.
A final stdin redirect is allowed for non-interactive runs: ... < /inputs/... or ... < /aux/... (no other redirects).
Inputs under /inputs; keep outputs under /outputs.
Working directory is /outputs; prefer relative paths for output files (e.g. -p topol.top) so tools like gmx solvate can safely rewrite topology files.

Interactive prompts

Some tools prompt for a group selection (e.g. gmx genion, gmx trjconv, gmx energy). SubSeq runs GROMACS non-interactively, so provide selections via stdin redirection from a file you upload to /inputs or /aux.

Example: genion (select solvent group, commonly SOL):

gmx genion ... < /aux/genion.stdin

gmx trjconv -center prompts twice (center group, then output group), so the stdin file must contain 2 lines. Do not reuse genion.stdin for trjconv.

Aux stdin files:

/aux/genion.stdin:
SOL

/aux/trjconv.stdin:
Protein
Protein

gmx trjconv ... -center ... < /aux/trjconv.stdin

Force fields

Available force fields: amber03, amber94, amber96, amber99, amber99sb-ildn, amber99sb, amberGS, charmm27, gromos43a1, gromos43a2, gromos45a3, gromos53a5, gromos53a6, gromos54a7, oplsaa. Use -ff <name> with pdb2gmx.

Quick relaxation

gmx pdb2gmx -f /inputs/protein/protein.pdb -o protein_processed.gro -p topol.top -ff charmm27 -water tip3p
	gmx grompp -f /inputs/protein/minim.mdp -c protein_processed.gro -p topol.top -o /outputs/relax.tpr -po /outputs/relax_mdout.mdp
gmx mdrun -s /outputs/relax.tpr -deffnm /outputs/relax -nb gpu -pme gpu -bonded gpu -update gpu -pin auto -v

Solvate and equilibrate

gmx pdb2gmx -f /inputs/enzyme/enzyme.pdb -o enzyme_processed.gro -p topol.top -ff amber99sb-ildn -water tip3p
gmx editconf -f enzyme_processed.gro -o enzyme_box.gro -bt triclinic -d 1.0 -c
gmx solvate -cp enzyme_box.gro -cs spc216.gro -p topol.top -o enzyme_solv.gro
gmx grompp -f /inputs/enzyme/nvt.mdp -c enzyme_solv.gro -p topol.top -r enzyme_solv.gro -o /outputs/enzyme_nvt.tpr -po /outputs/enzyme_nvt_mdout.mdp
gmx mdrun -s /outputs/enzyme_nvt.tpr -deffnm /outputs/enzyme_nvt -nb gpu -pme gpu -pin auto
gmx grompp -f /inputs/enzyme/npt.mdp -c /outputs/enzyme_nvt.gro -t /outputs/enzyme_nvt.cpt -p topol.top -o /outputs/enzyme_npt.tpr -po /outputs/enzyme_npt_mdout.mdp
gmx mdrun -s /outputs/enzyme_npt.tpr -deffnm /outputs/enzyme_npt -nb gpu -pme gpu -pin auto

Restart and analyze

gmx mdrun -s /inputs/production/production.tpr -cpi /inputs/production/production.cpt -deffnm /outputs/production_restart -nb gpu -pme gpu -bonded gpu -update gpu -pin auto
	gmx trjconv -s /outputs/production_restart.tpr -f /outputs/production_restart.xtc -o /outputs/production_centered.xtc -pbc mol -center < /aux/trjconv.stdin
	gmx rms -s /outputs/production_restart.tpr -f /outputs/production_centered.xtc -o /outputs/production_rmsd.xvg
	gmx eneconv -f /outputs/production_restart.edr -o /outputs/production_smoothed.edr