You will need to load the GNU compiler module, build Charm++ for mpi-crayxt and NAMD for CRAY-XT-g++, use the following command in your batch script:
aprun -n $PBS_NNODES -cc cpu namd2
To reduce memory usage, build Charm++ mpi-crayxt-smp instead and use (assuming you have 12 cores per node on your machine):
setenv MPICH_PTL_UNEX_EVENTS 100000 @ NPROC = $PBS_NNODES / 12 aprun -n $NPROC -N 1 -d 12 namd2 +ppn 11 +setcpuaffinity +pemap 1-11 +commap 0
For two processes per node (for possibly better scaling) use:
setenv MPICH_PTL_UNEX_EVENTS 100000 @ NPROC = $PBS_NNODES / 6 aprun -n $NPROC -N 2 -d 6 namd2 +ppn 5 +setcpuaffinity \ +pemap 1-8,10,11 +commap 0,9 ...
For three processes per node use:
setenv MPICH_PTL_UNEX_EVENTS 100000 @ NPROC = $PBS_NNODES / 4 aprun -n $NPROC -N 3 -d 4 namd2 +ppn 3 +setcpuaffinity \ +pemap 1-5,7,8,10,11 +commap 0,6,9 ...
The strange +pemap and +commap settings place the communication threads on cores that have been observed to have higher operating system loads.