View source for HPC/Applications/namd

== Introduction ==

[http://www.ks.uiuc.edu/Research/namd/ 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 [http://www.ks.uiuc.edu/Research/namd/license.html 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
:<pre>
:$ 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
:</pre>
: Version 2.6 is the CVS development version, and [http://www.ks.uiuc.edu/Research/namd/2.7b1/announce.html NAMD 2.7b1]  the subsequently released official version.
* Add the following to the end of your <code>~/.bashrc</code> file:
:<pre>
:module switch openmpi openmpi/1.3-intel10-4
:module load namd
:</pre>
: and ''also'' issue it on the command line (or simply re-login).  The program will be available under the name <code>namd2</code>.
* Verify  availability
:<pre>
:$ type -p namd2
:/opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2</pre>
: 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 <code>module</code> command to select appropriate versions.

=== Special instructions ===
* NAMD uses its own MPI wrapper, called [http://charm.cs.uiuc.edu/ Charm++].  Instead of "mpirun" in the [[HPC/Getting_started#Example job file|PBS example job]] use:
:<pre>
:...
:charmrun +p $NPROCS namd2 ...</pre>

== Documentation ==
* See ''Documentation'' on the [http://www.ks.uiuc.edu/Research/namd/ NAMD home page] – contains official [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ User guide] 
* Local documentation:
:<pre>$ ls $NAMD_HOME/share/doc
: README.txt  announce.txt  license.txt  notes.txt  ug.pdf</pre>