gromacs
Link to section 'Description' of 'gromacs' Description
GROMACS GROningen MAchine for Chemical Simulations is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.
Link to section 'Versions' of 'gromacs' Versions
- Bell: 2018.4, 2019.2
- Brown: 2018.4, 2019.2
- Scholar: 2018.4, 2019.2
- Gilbreth: 2018.4
- Negishi: 2022.3
- Anvil: 2021.2
Link to section 'Module' of 'gromacs' Module
You can check available gromacs version by:
module spider gromacs
You can check how to load the gromacs module by the module's full name:
module spider gromacs/XXXX
Note: RCAC also installed some containerized gromacs modules.
To use these containerized modules, please following the instructions in the output of "module spider gromacs/XXXX"
You can load the modules by:
module load gromacs # for default version
module load gromacs/XXXX # for specific version
Link to section 'Usage' of 'gromacs' Usage
The GROMACS executable is gmx_mpi and you can use gmx help commands for help on a command.
For more details about how to run GROMACS, please check GROMACS.
Link to section 'Example job' of 'gromacs' Example job
#!/bin/bash
# FILENAME: myjobsubmissionfile
#SBATCH --nodes=2 # Total # of nodes
#SBATCH --ntasks=256 # Total # of MPI tasks
#SBATCH --time=1:30:00 # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
# Manage processing environment, load compilers and applications.
module purge
module load gcc/XXXX openmpi/XXXX # or module load intel/XXXX impi/XXXX | depends on the output of "module spider gromacs/XXXX"
module load gromacs/XXXX
module list
# Launch MPI code
gmx_mpi pdb2gmx -f my.pdb -o my_processed.gro -water spce
gmx_mpi grompp -f my.mdp -c my_processed.gro -p topol.top -o topol.tpr
srun -n $SLURM_NTASKS gmx_mpi mdrun -s topol.tpr
Link to section 'Note' of 'gromacs' Note
#!/bin/bash
# FILENAME: myjobsubmissionfile
#SBATCH --nodes=2 # Total # of nodes
#SBATCH --ntasks=256 # Total # of MPI tasks
#SBATCH --time=1:30:00 # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
# Manage processing environment, load compilers and applications.
module purge
module load gcc/XXXX openmpi/XXXX # or module load intel/XXXX impi/XXXX | depends on the output of "module spider gromacs/XXXX"
module load gromacs/XXXX
module list
# Launch MPI code
gmx_mpi pdb2gmx -f my.pdb -o my_processed.gro -water spce
gmx_mpi grompp -f my.mdp -c my_processed.gro -p topol.top -o topol.tpr
srun -n $SLURM_NTASKS gmx_mpi mdrun -s topol.tpr
Using mpirun -np $SLURM_NTASKS gmx_mpi or mpiexex -np $SLURM_NTASKS gmx_mpi may not work for non-exclusive jobs on some clusters. Use srun -n $SLURM_NTASKS gmx_mpi or mpirun gmx_mpi instead. mpirun gmx_mpi without specifying the number of ranks will automatically pick up the number of SLURM_NTASKS and works fine.