NAMD/Batch

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All NAMD calculations should be submitted as a batch job to the batch system. To run a simulation with an input file input.in use the following command:

bsub [LSF options] "namd2 input.in"

By default the output will be found in the lsf.oXXXXXXX output file where XXXXXXX corresponds to the job ID of the job. The [LSF options] needs to be replaced with LSF parameters for the resource requirements of the job. For example,

bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in"

will request a runtime of up to 12 hours and only 500 MB of RAM.

Jobs that can run on a single node (24 cores) can be submitted in a similar way:

bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in"