NAMD

module avail namd/
module avail namd3.0_alpha9/

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Usage

License

To use the application, you first need to accept its license.

Paralellization

NAMD uses special type of parallelization mechanism. Although it depends on OpenMPI, you should use that with special treatment when running through multiple nodes:

mpirun --map-by node:PE=$PBS_NCPUS namd2 ++ppn $((PBS_NCPUS-1)) <configuration_file>

It's good to use less nodes with many cores for a good performance.

NAMD + Orca

For use NAMD with the support of Orca just directly add the path to orca binary to the configuration file and avoid using 'modoule add orca-4.2.1' as this is done automatically via the wrapper script. For details see the Orca page.

For effective run of NAMD + Orca QMMM combination it is necessary to run namd2 a bit differently: namd2 releases only one processor while running the QM program so the job should have (namdproc+qmgroups*(orcaprocs-1)) processors in common. Where orcaprocs is set by qmConfigLine "%%pal nprocs XY end" and namd2 should be run without +setcpuaffinity.