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.
Usage
Add module: module load gromacs/5.1.2
...
| Version | module | notes |
|---|---|---|
| 2020.4 | gromacs/2020.4 | |
| 2020.4 | gromacs/2020.4-plumed | with plumed support |
Required modules
- CPU version
- intel/20.0.3
- mvapich2/2.3.4 OR mpich/3.3.2
- GPU version
- intel/19.0.3
- cuda/10.2.89
- mvapich2/2.3.4 OR mpich/3.3.2
| Code Block | ||
|---|---|---|
| ||
srun $(which gmx_mpi) (gromacs programs) |
Benchmarks (on im1080 partition) indicated that best performance for mdrun is obtained using 4 OpenMP threads per MPI process. The usage for mdrun should be modified as follows
| Code Block | ||||
|---|---|---|---|---|
|
...
| |||
export OMP_NUM_THREADS=4 |
...
srun --ntasks-per-node=6 $(which gmx_mpi) mdrun (mdrun options) -ntomp 4 |
Benchmarks
Which version of Gromacs should I use?
Links
See http://manual.gromacs.org/programs/byname.html for a list of gromacs programs and how to run the programs
Absolute path to gromacs (gmx_mpi) executable: /share/Apps/gromacs/5.1.2/intel-16.0.3-mvapich2-2.1/bin/gmx_mpi
Benchmarks
...
