For small numbers of processors (1-8) use the non-MPI version of namd2. If your stack size limit is unlimited, which DQS may do, you will need to set it with ``limit stacksize 64M'' to run on multiple processors. To run on <procs> processors call the binary directly with the +p option:
namd2 +p<procs> <configfile>
For better performance on larger numbers of processors we recommend that you use the MPI version of NAMD. To run this version, you must have MPI installed. Furthermore, you must set two environment variables to tell MPI how to allocate certain internal buffers. Put the following commands in your .cshrc or .profile file, or in your job file if you are running under a queuing system:
setenv MPI_REQUEST_MAX 10240 setenv MPI_TYPE_MAX 10240
Then run NAMD with the following command:
mpirun -np <procs> namd2 <configfile>