HPC/Applications/namd

Introduction

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.

Subject to Univ. of Illinois Non-Exclusive, Non-Commercial Use License.

The NAMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969).

NAMD on Carbon

Required reading

HPC/Getting_started

Modules

• Versions

$ module avail namd

------------------------------- /opt/soft/modulefiles -------------------------------

namd/2.6.2009-02-11-Linux-x86_64-MPI-icc-1(default)

namd/2.7b1-MPI-icc-1

Version 2.6 is the CVS development version, and NAMD 2.7b1 the subsequently released official version.

• Add the following to the end of your ~/.bashrc file:

module switch openmpi openmpi/1.3-intel10-4

module load namd

and also issue it on the command line (or simply re-login). The program will be available under the name namd2.

• Verify availability

$ type -p namd2

/opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2

Note: This step is solely meant to verify that the binary is reachable simply by its name. As with other applications, do not call it directly, as the paths are version dependent. Use the module command to select appropriate versions.

Special instructions

• NAMD uses its own MPI wrapper, called Charm++. Instead of "mpirun" in the PBS example job use:

...

charmrun +p $NPROCS namd2 ...

Documentation

• See Documentation on the NAMD home page – contains official User guide
• Local documentation:

$ ls $NAMD_HOME/share/doc

README.txt announce.txt license.txt notes.txt ug.pdf