QuickStart GROMACS

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.

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$ module avail GROMACS

------------------------- /data/Apps/Modules/Software --------------------------

GROMACS/2016.1  GROMACS/2018  GROMACS/2018-CUDA  

$ module load GROMACS

Loading GROMACS/2016.1

  Loading requirement: Intel/17.0.1

$ whereis gmx

gmx: /data/Apps/gromacs/2016.1/bin/gmx

To read your tpr file, use $ % gmxdump -s your_tpr_file.tpr | more

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job submission script

 

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$ qsub gromacs_example.pbs

$ qstat