# Gromacs Server

## GROMACS Server

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</div>### Official Documentation:

<div id="bkmrk-https%3A%2F%2Fmanual.groma">https://manual.gromacs.org/current/user-guide/index.html</div><div id="bkmrk--1">  
</div><div id="bkmrk--2">  
</div>### Gromacs Server and Environment:

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</div><div id="bkmrk-gromacs-is-pre-insta">Gromacs is pre-installed on a Levich server and user accounts are initilized to include Gromacs path.</div><div id="bkmrk--4">  
</div><div id="bkmrk-in-case-you-want-to-">In case you want to see how the Gromacs environment was set, Here it is:</div><div id="bkmrk-in-file-%7E%2F.profile%2C-">In file ~/.profile, the last line points to gromacs environment initialization:</div><div id="bkmrk-source-%2Fusr%2Flocal%2Fgr">`source /usr/local/gromacs/bin/GMXRC`</div><div id="bkmrk--5">  
</div><div id="bkmrk--6">  
</div><div id="bkmrk-users-are-expected-t">**Users are expected to install their own Python and Python modules.**</div><div id="bkmrk--7">  
</div><div id="bkmrk-install-conda-python">Install Conda Python and Python modules:</div><div id="bkmrk-wget-https%3A%2F%2Frepo.an">`wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh`</div><div id="bkmrk-chmod-%2Bx-miniconda3-">`chmod +x Miniconda3-latest-Linux-x86_64.sh`</div><div id="bkmrk-.%2Fminiconda3-latest-">`./Miniconda3-latest-Linux-x86_64.sh ` (answer yes to initialize Minicoda3)</div><div id="bkmrk--8">  
</div><div id="bkmrk-logout-and-back-in-t">Logout and back in to have conda environment, then run:</div><div id="bkmrk--9">  
</div><div id="bkmrk-conda-install-numpy-">`conda install numpy scipy matplotlib pandas`</div><div id="bkmrk--10">  
</div><div id="bkmrk-conda-can-be-deactiv">Conda can be deactivated or reactivated by command:</div><div id="bkmrk-conda-deactivate">`conda deactivate`</div><div id="bkmrk-conda-activate">`conda activate`</div><div id="bkmrk--11">  
</div><div id="bkmrk--12">  
</div>### Gromacs Command

<div id="bkmrk-main-command%3A-gmk">Main Command: `gmk`</div>#### Examples: 

<div id="bkmrk-gmx--h%C2%A0%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0">`gmx -h ` (print help)</div><div id="bkmrk-gmk--v%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0-%C2%A0-">`gmk -v` (show version)</div><div id="bkmrk-gmx-help-%5Bmodule%5D%C2%A0-%C2%A0">`gmx help [module]` (documentation of a module)</div><div id="bkmrk--13">  
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