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

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

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

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