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:
The script is very similar to the bmdrun2016 file in the lysozyme folder. Only the "qc" resource has been removed.
#!/bin/csh #BSUB -n 2 #BSUB -R "span[ptile=2]" #BSUB -W 20 #BSUB -o out.%J #BSUB -e err.%J source /usr/local/apps/gromacs/gromacs2016-int2016.csh mpirun gmx_mpi mdrun -v -deffnm em
To submit the job, type
bsub < bmdrun
Last modified: May 24 2024 12:31:31.