GROMACS

2024.4

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2023.4

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2020.6

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2019.6

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2018.8

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GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.

For basic usage of the console environment, check the Terminal application.

Command-Line Reference

GROMACS includes several tools for preparing, running and analysing molecular dynamics simulations. These are invoked with commands like e.g. gmx grompp. Here gmx binary refers to GROMACS compiled with OpenMP support.

Different binaries are available wich corresponds to GROMACS compiled with different options (in addition to the OpenMP support). Accordingly, in the command line string, gmx should be replaced with:

• gmx_mpi for using the MPI version of GROMACS

• gmx_gpu for using GROMACS with GPU acceleration support

• gmx_gpu_mpi for hybrid/heterogeneous acceleration support.

Batch Mode

Use this option to submit a Bash script (*.sh) which will execute GROMACS commands after the job starts. The job will close after the execution of the program.