Gromacs Server

GROMACS Server

Official Documentation:

https://manual.gromacs.org/current/user-guide/index.html

Gromacs Server and Environment:

Gromacs is pre-installed on a Levich server and user accounts are initilized to include Gromacs path.

In case you want to see how the Gromacs environment was set, Here it is:

In file ~/.profile, the last line points to gromacs environment initialization:

source /usr/local/gromacs/bin/GMXRC

Users are expected to install their own Python and Python modules.

Install Conda Python and Python modules:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

chmod +x Miniconda3-latest-Linux-x86_64.sh

./Miniconda3-latest-Linux-x86_64.sh   (answer yes to initialize Minicoda3)

Logout and back in to have conda environment, then run:

conda install numpy scipy matplotlib pandas

Conda can be deactivated or reactivated by command:

conda deactivate

conda activate

Gromacs Command

Main Command: gmk

Examples:

gmx -h

                                        (print help)

gmk -v                                           (show version)

gmx help [module]                   (documentation of a module)