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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
| Version | module name | notes |
|---|---|---|
| 2020.4 | gromacs/2020.4 | |
| 2020.4 | gromacs/2020.4-plumed | with plumed support |
Required modules
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- intel/20.0.3
- mvapich2/2.3.4 OR mpich/3.3.2
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| 2021.4 | gromacs/2021.4 | |
| 2021.4 | gromacs/2021.4-plumed | with plumed support |
| 2021.4 | gromacs/2021.4-cuda-11.6.0 | gpu enabled |
| 2021.4 | gromacs/2021.4-plumed-cuda-11.6.0 | gpu enabled with plumed support |
Required modules
- intel/2021.3.0
- mvapich2/2.3.4 OR mpich/3.3.2
- For Plumed support
- plumed/2.7.3
- For GPU version
- cuda/11.6.0
| Code Block | ||
|---|---|---|
| ||
srun $(which gmx_mpi) (gromacs programs) |
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| 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
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