HPC/Applications/namd: Difference between revisions
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== NAMD on Carbon == | == NAMD on Carbon == | ||
=== Required reading === | |||
[[HPC/Getting_started]] | |||
=== Modules === | === Modules === | ||
* Add the following to the end of your <code>~/.bashrc</code> file: | * Add the following to the end of your <code>~/.bashrc</code> file: | ||
:<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 | : 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 | * Verify availability | ||
:<pre>$ type -p namd2 | :<pre>$ type -p namd2 | ||
Revision as of 18:09, 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.
- 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