Gromacs Server
GROMACS Server and Quick Start
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)