HPC/Applications/namd: Difference between revisions
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:<pre>module load namd</pre> | :<pre>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>. | : and ''also'' issue it on the command line (or simply re-login). The program will be available under the name <code>namd2</code>. | ||
* Versions | |||
:<pre>$ module avail namd | |||
:--------------------------------------------------- /opt/soft/modulefiles --------------------------------------------------- | |||
:namd/2.6.2009-02-11-Linux-x86_64-MPI-icc-1</pre> | |||
: This version is the CVS 2.6+ development version. [http://www.ks.uiuc.edu/Research/namd/2.7b1/announce.html NAMD 2.7b1 has been released] recently and will be installed shortly. | |||
* Verify availability | * Verify availability | ||
:<pre>$ type -p namd2 | :<pre>$ type -p namd2 | ||
:/opt/soft/namd-2.6.2009-02-11-Linux-x86_64-MPI-icc-1/bin/namd2</pre> | :/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 === | === 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: | * 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: | ||
Revision as of 18:18, April 2, 2009
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
Modules
- Add the following to the end of your
~/.bashrcfile:
module load namd
- and also issue it on the command line (or simply re-login). The program will be available under the name
namd2.
- Versions
$ module avail namd
- --------------------------------------------------- /opt/soft/modulefiles ---------------------------------------------------
- namd/2.6.2009-02-11-Linux-x86_64-MPI-icc-1
- This version is the CVS 2.6+ development version. NAMD 2.7b1 has been released recently and will be installed shortly.
- 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
modulecommand 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