GROMACS

Overview

GROMACS is a package for computing molecular dynamics, simulating Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed for biochemical molecules with complicated bonded interactions (e.g. proteins, lipids, nucleic acids) but can also be used for non-biological systems (e.g. polymers).

Several versions of GROMACS are compiled with various versions of the Intel compiler. The Intel MKL library associated with the compiler provides FFT functions. The following GROMACS flavours are built (not necessarily all available in all versions – check specific version documentation below):

• Single and double precision multi-threaded (OpenMP) versions: mdrun and mdrun_d
• AVX-optimized versions of the above multi-threaded executables for use on Ivybridge (or better) Intel nodes.
• Single and double precision MPI (not threaded) versions: mdrun_mpi and mdrun_d_mpi
• GPU versions

The specific version documentation listed below gives full details of which modulefiles to load and how to run GROMACS. Your jobscripts must request the correct Intel nodes otherwise GROMACS may run inefficiently or not at all.

2016.3

Please see the GROMACS v2016.3 CSF3 documentation.

2016.4 (with and without Plumed Plugin)

Please see the GROMACS v2016.4 CSF documentation.

2018.4 (with GPU builds)

Please see the GROMACS v2018.4 CSF documentation.

2020.1 (with GPU builds)

Please see the GROMACS v2020.1 CSF documentation.

2020.3 (with GPU builds)

Please see the GROMACS v2020.3 CSF documentation.

2021.5 (with GPU builds)

Please see the GROMACS v2021.5 CSF documentation.

Legacy Version

We recommend using one of the versions of Gromacs listed above; however, a legacy (unsupported) version of 4.6.7 is available. Please see the GROMACS 4.6.7 CSF documentation.

Useful info

The information here is usually applicable to more than one version of the software. Information specific to a version will always be given on that page.

File locking error

If you get the following error:

Source file: src/gromacs/fileio/checkpoint.cpp (line 2493)
Fatal error:
File locking is not supported on this system. Use -noappend or specify -append

then this is because we do not support file locking on the scratch (Lustre) filesystem. We recommend that you submit the job again with the -noappend option enabled.