You need to submit your NAMD calculations in batch mode, through 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 you can find the output in the lsf.oXXXXXXX output file where XXXXXXX corresponds to the job ID of the job. You need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. 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"