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Coarse-Grained Simulation with GROMACS

Getting Started

Download the necessary files from this Google Drive folder.

Load Required Modules on Rivanna

module load gcc/11.4.0 openmpi/4.1.4 gromacs/2023.2
module spider gromacs/2023.2
pip install --user vermouth
export PATH=$PATH:/home/YOUR_COMPUTING_ID/.local/bin

Step 1: Create Coarse-Grained Peptide

Convert the atomistic peptide PDB file to a coarse-grained model using martinize2.

martinize2 -f KYFIL.pdb -x KYFIL_CG.pdb -o single_KYFIL.top -ff martini3001 -ss C -cter NH2-ter

Flags:

  • -ff: Force field (martini3001)
  • -ss: Secondary structure (use C for coil)
  • -cter: Terminus (NH2 amidation at C-terminus)

Step 2: Convert PDB to GRO

gmx_mpi editconf -f KYFIL_CG.pdb -o KYFIL_CG.gro -d 0.5

Adds a 0.5 nm buffer around the peptide.

Step 3: Create Peptide Grid

gmx_mpi genconf -f KYFIL_CG.gro -nbox 4 4 4 -rot yes -dist 1 2 1 -o KYFIL_64_box_cg.gro

Notes:

  • 64 peptides total (4 × 4 × 4)
  • Randomly rotates each peptide
  • Spacing defined by -dist in nm (x y z)

Step 4: Solvate the Box

gmx_mpi solvate -cp KYFIL_64_box_cg.gro -cs water.gro -o Grid_KYFIL_CG_water.gro -box 13 13 13

Adds coarse-grained water (1 bead = 4 water molecules).

Example output:

  • \~18,674 water molecules
  • Volume ≈ 2197 nm³
  • Density ≈ 2614 g/L

Step 5: Prepare Topology File

  1. Copy single_KYFIL.top to system.top
  2. Open system.top and edit it to include:
#include "martini_v3.0.0.itp"
#include "martini_v3.0.0_solvents_v1.itp"
#include "martini_v3.0.0_ions_v1.itp"
#include "molecule_0.itp"

[ system ]
Title of the system

[ molecules ]
molecule_0    64
W             [# water molecules]

Replace [ # water molecules ] with the number from:

grep -c W Grid_KYFIL_CG_water.gro

Step 6: Add Ions

Generate the input file for ion addition:

gmx_mpi grompp -f ions.mdp -c Grid_KYFIL_CG_water.gro -p system.top -o ions.tpr

Add NaCl to 0.15 M concentration:

gmx_mpi genion -s ions.tpr -pname NA -nname CL -neutral -conc 0.15 -o Grid_KYFIL_CG_ion.gro

Choose group 13 (water) when prompted.

Get updated atom counts:

grep -c W Grid_KYFIL_CG_ion.gro
grep -c CL Grid_KYFIL_CG_ion.gro
grep -c NA Grid_KYFIL_CG_ion.gro

Update system.top again:

[ molecules ]
molecule_0    64
W             18150
CL            326
NA            198

Step 7: Energy Minimization

Prepare:

gmx_mpi grompp -f minimization.mdp -c Grid_KYFIL_CG_ion.gro -p system.top -o minimization.tpr -maxwarn 2

Submit using a SLURM script:

#!/bin/bash
#SBATCH --nodes=7
#SBATCH --ntasks-per-node=36
#SBATCH --mail-user=YOUR_COMPUTING_ID@virginia.edu
#SBATCH --mail-type=END,FAIL,TIME_LIMIT
#SBATCH --time=3-00:00:00
#SBATCH --partition=parallel
#SBATCH -A YOUR_ALLOCATION
#SBATCH -o minimize.out

module purge
module load gcc/11.4.0 openmpi/4.1.4 gromacs/2023.2
gmx mdrun -v -deffnm minimization

Step 8: Run Dynamics

Preprocess for dynamics:

gmx_mpi grompp -f dynamic.mdp -c minimization.gro -p system.top -o dynamic.tpr

Submit dynamics run with:

#!/bin/bash
#SBATCH --nodes=7
#SBATCH --ntasks-per-node=36
#SBATCH --mail-user=YOUR_COMPUTING_ID@virginia.edu
#SBATCH --mail-type=END,FAIL,TIME_LIMIT
#SBATCH --time=3-00:00:00
#SBATCH --partition=parallel
#SBATCH -A YOUR_ALLOCATION
#SBATCH -o dynamic.out

module purge
module load gcc/11.4.0 openmpi/4.1.4 gromacs/2023.2
gmx mdrun -v -deffnm dynamic

Your simulation is now set up and running.