NAMD User Guide



Version 1.5






R. Brunner, A. Dalke, A. Gursoy, W. Humphrey, M. Nelson


September 6, 1998






Theoretical Biophysics Group
University of Illinois and Beckman Institute
405 N. Mathews
Urbana, IL 61801

Description

The NAMD User Guide describes how to run and use the various features of the molecular dynamics program NAMD. This guide includes the capabilities of the program, how to use these capabilities, the necessary input files and formats, and how to run the program both on uniprocessor machines and in parallel.

NAMD Version 1.5

Authors: Robert Brunner, Andrew Dalke, Attila Gursoy,
Bill Humphrey, and Mark Nelson

Theoretical Biophysics Group, Beckman Institute, University of Illinois.

©1995-97 The Board of Trustees of the University of Illinois
All Rights Reserved

NOTICE

The program NAMD is not in the public domain. However, it is freely available without fee for education, research, and commercial purposes. By obtaining copies of this and other files that comprise the NAMD program, you, the Licensee, agree to abide by the following conditions and understandings with respect to the copyrighted software:

1.

The software is copyrighted in the name of the Board of Trustees of the University of Illinois (UI), and ownership of the software remains with the UI.

2.

Permission to use and modify this software and its documentation is hereby granted to Licensee. In addition, permission to copy this work and any derived works is granted to Licensee, provided that

(a)

the copyright notice and this permission notice appear on all such copies,

(b)

that proper credit be given by citing

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. Skeel and K. Schulten. NAMD - A parallel, object-oriented molecular dynamics program. J. Supercomputing App., 10:251-268, 1996.

for NAMD and

W. T. Rankin and J. A. Board, Jr., Tech Rept. 95-002, EE Dept., Duke Univ.

for DPMTA

(c)

that NAMD and any derived works are not redistributed for a fee,

(d)

that programs derived from NAMD be given a different name.

3.

Licensee may not use the name, logo, or any other symbol of the UI nor the names of any of its employees nor any adaptation thereof in advertizing or publicity pertaining to the software without specific prior written approval of the UI.

4.

THE UI MAKES NO REPRESENTATIONS ABOUT THE SUITABILITY OF THE SOFTWARE FOR ANY PURPOSE. IT IS PROVIDED "AS IS" WITHOUT EXPRESS OR IMPLIED WARRANTY.

5.

The UI shall not be liable for any damages suffered by Licensee from the use of this software.