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 Sandybridge and Ivybridge Intel nodes.
• Single and double precision MPI (not threaded) versions: mdrun_mpi and mdrun_d_mpi
• GPU versions will be available soon

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.

4.5.4 (with and without a g_hbond bugfix)

Please see the GROMACS v4.5.4 CSF documentation.

4.6.1 (with and without the Plumed 1.3 plugin)

Please see the GROMACS v4.6.1 CSF documentation.

4.6.7

Please see the GROMACS v4.6.7 CSF documentation.

5.0.4

Please see the GROMACS v5.0.4 CSF documentation.

5.1.4

Please see the GROMACS v5.1.4 CSF documentation.

2016.3

Please see the GROMACS v2016.3 CSF documentation.

2018.3 (GPU)

Please see the GROMACS v2018.3 CSF documentation.