User Tools

Site Tools


gromacs-software

Gromacs

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.

Information

Usage

See versions of gromacs which are available:

$ module avail gromacs

Load a particular version into your environment and run it:

$ module load gromacs/2018.2
$ gmx

Note: Please use the -nt option to limit the number of threads launched by gmx to be the same amount as in your SLURM sbatch allocation. See the gromacs documentation for more information.

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz
$ tar xf gromacs-2018.2.tar.gz
$ cd gromacs-2018.2
$ mkdir build
$ cd build
$ sudo yum install fftw-devel.x86_64
$ cmake3 .. -DCMAKE_INSTALL_PREFIX=/export/apps/gromacs/2018.2
$ make
$ sudo mkdir -p /export/apps/gromacs/2018.2
$ sudo chown aorth /export/apps/gromacs/2018.2
$ make install
$ sudo chown -R root:root /export/apps/gromacs/2018.2

Gromacs recommends sourcing the GMXRC.bash script to set up the user's environment, but since we're using environment modules we can't do that. Instead, I compared the output env before and after loading the GMXRC.bash environment and then used that to create the module file.

gromacs-software.txt · Last modified: 2019/11/11 17:48 by aorth