NAMD
Description
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. 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.
License
To use the application, you first need to accept its license.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of namd and load default version of namd as
module avail namd/ # list available modules module load namd # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail namd
and choose explicit version you want to use.
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 different: 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.