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  1. OIT HPC
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  3. GROMACS

    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.

    See the GROMACS Tutorial Lysosome in Water, to get started.

    Copy the example files from /home/gwhowell/apps/samples/gromacs/lysozyme and then cd to lysozyme.

    Create a submission script called bmdrun containing the following:

     
    #!/bin/csh
    #BSUB -n 16
    #BSUB -R "!dc && !qc" 
    #BSUB -W 20
    #BSUB -o out.%J
    #BSUB -e err.%J
    source /usr/local/apps/gromacs/GMXRC-511.csh
    mpirun gmx_mpi mdrun -v -deffnm em
    
    To submit the job, type

    bsub < bmdrun
    

    Last modified: June 19 2020 11:03:32.

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