Computing

Description

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.

Availability

Definitely installed on sinister.

Source

http://www.ks.uiuc.edu/Research/namd/

Licence details

NAMD is open source but commercial use isn't permitted. The licence explains how to cite it. The full licence text can be found at the bottom of this page.

Instructions for users

The tutorial files are kept in /usr/local/namd/namd-tutorial-files.

You probably want to load the multicore version and use that over 12 cores on the newer machines.

module add namd/multicore
namd2 +p12 configfile


If you want to do anything fancier, have a look at http://www.ks.uiuc.edu/Research/namd/2.8/notes.html for running over more than one machine and use the TCP version.

Documentation

Online user's guide at http://www.ks.uiuc.edu/Research/namd/2.8/ug/.

Comes precompiled. Untar it and go. If you really want to build it, have a look at the notes on the local wiki.

Full licence text

University of Illinois
NAMD Molecular Dynamics Software

Upon execution of this Agreement by the party identified below ("Licensee"),
The Board of Trustees of the University of Illinois  ("Illinois"), on behalf
of The Theoretical Biophysics Group ("TBG") in the Beckman Institute, will
provide the NAMD molecular dynamics software ("NAMD") in Executable Code
and/or Source Code form ("Software") to Licensee, subject to the following
terms and conditions. For purposes of this Agreement, Executable Code is the
compiled code, which is ready to run on Licensee's computer. Source code
consists of a set of files which contain the actual program commands that are
compiled to form the Executable Code.

1. The Software is intellectual property owned by Illinois, and all right,
title and interest, including copyright, remain with Illinois.  Illinois
grants, and Licensee hereby accepts, a restricted, non-exclusive,
internal business purposes only, e.g. not for commercial use (see Clause 7
below), without a fee.

2. Licensee may, at its own expense, create and freely distribute
complimentary works that interoperate with the Software, directing others to
the TBG server to license and obtain the Software itself. Licensee may, at
its own expense, modify the Software to make derivative works.  Except as
explicitly provided below, this License shall apply to any derivative work
as it does to the original Software distributed by Illinois.  Any derivative
work should be clearly marked and renamed to notify users that it is a
modified version and not the original Software distributed by Illinois.
markings on any derivative work and to include in the documentation of such
work the acknowledgement:

"This software includes code developed by the Theoretical Biophysics Group
in the Beckman Institute for Advanced Science and Technology at the
University of Illinois at Urbana-Champaign."

Licensee may redistribute without restriction works with up to 1/2 of their
non-comment source code derived from at most 1/10 of the non-comment source
code developed by Illinois and contained in the Software, provided that the
above directions for notice and acknowledgement are observed.  Any other
distribution of the Software or any derivative work requires a separate
negotiate an appropriate license for such distribution.

3. Except as expressly set forth in this Agreement, THIS SOFTWARE IS PROVIDED
"AS IS" AND ILLINOIS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF
ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES
OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF
THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK, OR OTHER RIGHTS.
LICENSEE ASSUMES THE ENTIRE RISK AS TO THE RESULTS AND PERFORMANCE OF THE
SOFTWARE AND/OR ASSOCIATED MATERIALS.  LICENSEE AGREES THAT UNIVERSITY SHALL
NOT BE HELD LIABLE FOR ANY DIRECT, INDIRECT, CONSEQUENTIAL, OR INCIDENTAL
DAMAGES WITH RESPECT TO ANY CLAIM BY LICENSEE OR ANY THIRD PARTY ON ACCOUNT
OF OR ARISING FROM THIS AGREEMENT OR USE OF THE SOFTWARE AND/OR ASSOCIATED
MATERIALS.

agrees to take all reasonable steps to insure that the Software is
protected and secured from unauthorized disclosure, use, or release and
will treat it with at least the same level of care as Licensee would use to
protect and secure its own proprietary computer programs and/or information,
but using no less than a reasonable standard of care.  Licensee agrees to
provide the Software only to any other person or entity who has registered
with Illinois. If licensee is not registering as an individual but as an
institution or corporation each member of the institution or corporation
who has access to or uses Software must agree to and abide by the terms
copying or use of the Software, Licensee shall promptly notify Illinois
in writing. Licensee expressly agrees to use the Software only in the
manner and for the specific uses authorized in this Agreement.

5. By using or copying this Software, Licensee agrees to abide by the
copyright law and all other applicable laws of the U.S. including, but not
limited to, export control laws and the terms of this license. Illinois
shall have the right to terminate this license immediately by written
notice upon Licensee's breach of, or non-compliance with, any
terms of the license. Licensee may be held legally responsible for any
copyright infringement that is caused or encouraged by its failure to
abide by the terms of this license. Upon termination, Licensee agrees to
destroy all copies of the Software in its possession and to verify such
destruction in writing.

6. The user agrees that any reports or published results obtained with
the Software will acknowledge its use by the appropriate citation as
follows:

"NAMD was developed by the Theoretical Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign."

Any published work which utilizes NAMD shall include the following reference:

"James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart,
Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel,
Laxmikant Kale, and Klaus Schulten.  Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005."

Electronic documents will include a direct link to the official NAMD page
at http://www.ks.uiuc.edu/Research/namd/

7. Commercial use of the Software, or derivative works based thereon,
use of the Software, Licensee will contact Illinois (namd@ks.uiuc.edu) to
negotiate an appropriate license for such use. Commercial use includes:
(1) integration of all or part of the Software into a product for sale,
lease or license by or on behalf of Licensee to third parties, or
(2) distribution of the Software to third parties that need it to

8. Government Rights. Because substantial governmental funds have been
used in the development of NAMD, any possession, use or sublicense of the
Software by or to the United States government shall be subject to such
required restrictions.

9. NAMD is being distributed as a research and teaching tool and as
such, TBG encourages contributions from users of the code that might, at
Illinois' sole discretion, be used or incorporated to make the basic
operating framework of the Software a more stable, flexible, and/or useful
product.  Licensees who contribute their code to become an internal
portion of the Software agree that such code may be distributed by
Illinois under the terms of this License and may be required to sign an
"Agreement Regarding Contributory Code for NAMD Software" before Illinois
can accept it (contact namd@ks.uiuc.edu for a copy).

UNDERSTOOD AND AGREED.

Contact Information:

The best contact path for licensing issues is by e-mail to
namd@ks.uiuc.edu or send correspondence to:
NAMD Team
Theoretical Biophysics Group
Beckman Institute
University of Illinois
405 North Mathews MC-251
Urbana, Illinois 61801 USA
FAX: (217) 244-6078



System status

System monitoring page

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