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GROMACS with CHARMM36 Force Field

GROMACS 2025.4 is available on Sol with the CHARMM36 force field (February 2021) pre-installed. This build includes GPU acceleration via NVIDIA A100 GPUs and MPI parallelism for multi-node production runs.

Loading the Module​

module load gromacs/2025.4-gpu-mpi-charm

This module automatically loads its dependencies (GCC 12.1, CUDA 12.6, OpenMPI 4.1.5, FFTW 3.3.10) and sources the GROMACS environment (GMXRC).

Available Binaries​

BinaryPurpose
gmxSerial pre- and post-processing (pdb2gmx, editconf, solvate, genion, grompp, analysis tools)
gmx_mpiMPI-parallel mdrun for production simulations — use this in job scripts

Do not use gmx_mpi for setup and analysis steps. It is built mdrun-only and will not have those subcommands. Use gmx for everything except running the simulation itself.

The CHARMM36 Force Field​

Multiple CHARMM36 versions are pre-installed into the GROMACS topology directory — no manual download or GMXLIB path changes are needed. Pass the exact force field name to gmx pdb2gmx with -ff, or omit it and pick from the numbered list.

Installed CHARMM36 Versions​

Force Field NameReleaseNotes
charmm36-feb2021February 2021General-purpose; broad literature compatibility
charmm36-feb2026_cgenff-5.0February 2026Latest release; includes CGenFF 5.0

To confirm what is available in your session:

module load gromacs/2025.4-gpu-mpi-charm
gmx pdb2gmx -h 2>&1 | grep charmm36

Typical Workflow​

1. Prepare the Protein Topology​

Use pdb2gmx with CHARMM36 and the CHARMM-compatible TIP3P water model. Pass -ff with the exact force field name from the Installed CHARMM36 Versions table:

# February 2021 (broad literature compatibility)
gmx pdb2gmx \
  -f protein.pdb \
  -o protein_processed.gro \
  -water tip3p \
  -ff charmm36-feb2021

# February 2026 with CGenFF 5.0 (latest)
gmx pdb2gmx \
  -f protein.pdb \
  -o protein_processed.gro \
  -water tip3p \
  -ff charmm36-feb2026_cgenff-5.0

Omit -ff entirely to get an interactive numbered menu of all available force fields.

2. Define the Simulation Box​

gmx editconf \
  -f protein_processed.gro \
  -o protein_box.gro \
  -c \
  -d 1.2 \
  -bt dodecahedron

3. Solvate​

gmx solvate \
  -cp protein_box.gro \
  -cs spc216.gro \
  -o protein_solv.gro \
  -p topol.top

4. Add Ions​

# Generate a tpr for genion
gmx grompp \
  -f ions.mdp \
  -c protein_solv.gro \
  -p topol.top \
  -o ions.tpr

gmx genion \
  -s ions.tpr \
  -o protein_solv_ions.gro \
  -p topol.top \
  -pname NA \
  -nname CL \
  -neutral

5. Energy Minimization​

gmx grompp \
  -f minim.mdp \
  -c protein_solv_ions.gro \
  -p topol.top \
  -o em.tpr

gmx mdrun -v -deffnm em

6. Production MD​

For production runs, use gmx_mpi inside a SLURM job (see below).

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

Example SLURM Job Script​

The following script requests one A100 GPU and 16 MPI ranks (one per physical core pair) for a production MD run. Adjust --ntasks and --grompp options to fit your system.

#!/bin/bash
#SBATCH --job-name=gromacs_md
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:a100:1
#SBATCH --mem=64G
#SBATCH --time=24:00:00
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err

module purge
module load gromacs/2025.4-gpu-mpi-charm

# Run production MD
mpirun -np $SLURM_NTASKS gmx_mpi mdrun \
  -s md.tpr \
  -deffnm md \
  -ntmpi 1 \
  -ntomp $SLURM_CPUS_PER_TASK \
  -gpu_id 0 \
  -nb gpu \
  -pme gpu \
  -bonded gpu \
  -update gpu

Multi-Node Example​

#!/bin/bash
#SBATCH --job-name=gromacs_md_multinode
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:a100:1
#SBATCH --mem=64G
#SBATCH --time=48:00:00
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err

module purge
module load gromacs/2025.4-gpu-mpi-charm

mpirun -np $SLURM_NTASKS gmx_mpi mdrun \
  -s md.tpr \
  -deffnm md \
  -ntomp $SLURM_CPUS_PER_TASK \
  -nb gpu \
  -pme gpu \
  -bonded gpu

Small Molecules with CGenFF​

For ligands and small molecules not parameterized in CHARMM36, generate parameters using the CGenFF program (requires a free account at the ParamChem server):

  1. Upload your ligand MOL2 file to https://cgenff.umaryland.edu
  2. Download the output .str file
  3. Convert to GROMACS format with cgenff_charmm2gmx.py (available from the MacKerell lab GitHub)
  4. Include the resulting lig.itp and lig.prm in your topology
; In topol.top — include ligand parameters before the system definition
#include "lig.prm"
#include "lig.itp"

High penalty scores (> 50) in the CGenFF output indicate parameters that should be validated or refined before use in publication-quality work.

Key MDP Settings for CHARMM36​

CHARMM36 requires specific non-bonded settings. Use these in your .mdp files:

; Non-bonded interactions
cutoff-scheme       = Verlet
ns-type             = grid
nstlist             = 20
rlist               = 1.2
rcoulomb            = 1.2
rvdw                = 1.2
vdwtype             = Cut-off
vdw-modifier        = Force-switch
rvdw-switch         = 1.0

; Electrostatics
coulombtype         = PME
pme-order           = 4
fourierspacing      = 0.16

; Temperature and pressure coupling
tcoupl              = V-rescale
pcoupl              = C-rescale

The vdw-modifier = Force-switch with rvdw-switch = 1.0 is required for CHARMM36 accuracy. Using plain Cut-off without the force switch will produce incorrect results.

Useful Commands After a Run​

# Check energy conservation
gmx energy -f md.edr -o energy.xvg

# Extract a trajectory (remove PBC, center protein)
gmx trjconv -s md.tpr -f md.xtc -o md_nojump.xtc -pbc nojump -center

# Compute RMSD
gmx rms -s md.tpr -f md_nojump.xtc -o rmsd.xvg

# Compute RMSF
gmx rmsf -s md.tpr -f md_nojump.xtc -o rmsf.xvg -res

Additional Resources​