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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

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: 2018/07/16 18:48 by aorth