HPC/Applications/namd: Difference between revisions

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== NAMD on Carbon ==
== NAMD on Carbon ==
; Required reading: [[HPC/Getting_started]]
=== 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 "namd2".
: 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

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

...
charmrun +p$NPROCS namd2 ...

Documentation

$ ls $NAMD_HOME/share/doc
README.txt announce.txt license.txt notes.txt ug.pdf