GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Availability¶
| Software | Version | Dependent Toolchain | Module Load Command |
|---|---|---|---|
| GROMACS | 2021.5 | foss/2021b | module load foss/2021b GROMACS/2021.5 |
| GROMACS | 2021.5-CUDA-11.4.1 | foss/2021b | module load foss/2021b GROMACS/2021.5-CUDA-11.4.1 |
| GROMACS | 2024.1 | foss/2023b | module load foss/2023b GROMACS/2024.1 |
| GROMACS | 2023.1-CUDA-12.0.0 | foss/2022b | module load foss/2022b GROMACS/2023.1-CUDA-12.0.0 |
Application Information, Documentation¶
The documentation of GROMACS is available at GROMACS Manual, where you can find the tutorials in topologies, input file format, setting parameters, etc.
Using GROMACS¶
GROMACS can be used on CPU or GPU. When using GROMACS with GPUs (Graphics Processing Units), the calculations can be significantly accelerated, allowing for faster simulations. You can use GROMACS with GPU acceleration, but you need to use GPU nodes on our cluster.
Sample Batch Script to Run GROMACS on GPU gmx_gpu.submit.sh
#!/bin/bash -l
# NOTE the -l (login) flag!
#SBATCH -J gmx2023
#SBATCH -o test.%x.%j.out
#SBATCH -e test.%x.%j.err
#SBATCH --mail-type=ALL
#SBATCH --partition=gpu
#SBATCH --qos=standard
#SBATCH --time 72:00:00 # Max 3 days
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=2
#SBATCH --gpus-per-node=4
#SBATCH --account=PI_ucid # Replace PI_ucid with the UCID of PI, if you don't know PI's UCID use "sacctmgr show user username" on the login screen, replace "username" with your UCID
module purge
module load wulver
module load foss/2022b GROMACS/2023.1-CUDA-12.0.0
INPUT_DIR=${PWD}/INPUT
OUTPUT_DIR=${PWD}/OUTPUT
cp -r $INPUT_DIR/* $OUTPUT_DIR/
cd $OUTPUT_DIR
srun gmx_mpi mdrun -deffnm run -cpi -v -ntomp 2 -pin on -tunepme -dlb yes -nb gpu -noappend
Sample Batch Script to Run GROMACS on CPU gmx_cpu.submit.sh
#!/bin/bash -l
# NOTE the -l (login) flag!
#SBATCH -J gmx2021
#SBATCH -o test.%x.%j.out
#SBATCH -e test.%x.%j.err
#SBATCH --mail-type=ALL
#SBATCH --partition=general
#SBATCH --qos=standard
#SBATCH --time 72:00:00 # Max 3 days
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --account=PI_ucid # Replace PI_ucid with the UCID of PI, if you don't know PI's UCID use "sacctmgr show user username" on the login screen, replace "username" with your UCID
module purge
module load wulver
module load foss/2021b GROMACS/2021.5
INPUT_DIR=${PWD}/INPUT
OUTPUT_DIR=${PWD}/OUTPUT
cp -r $INPUT_DIR/* $OUTPUT_DIR/
cd $OUTPUT_DIR
srun gmx_mpi mdrun -v -deffnm em -cpi -v -ntomp 1 -pin on -tunepme -dlb yes -noappend
The tutorial in the above-mentioned job script can be found in
/apps/testjobs/gromacs
Related Applications¶
User Contributed Information¶
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