NAMD User's Guide



Version 3.0






Rafael Bernardi, Milind Bhandarkar, Abhinav Bhatele, Eric Bohm, W. Michael Brown, Robert Brunner, Ronak Buch, Floris Buelens, Haochuan Chen, Christophe Chipot, Jaemin Choi, Han-Yi Chou, David Clark, Andrew Dalke, Surjit Dixit, Giacomo Fiorin, Peter Freddolino, Haohao Fu, Paul Grayson, Justin Gullingsrud, Attila Gursoy, David Hardy, Chris Harrison, Jerome Hénin, William Humphrey, David Hurwitz, Antti-Pekka Hynninen, Barry Isralewitz, Nikhil Jain, Wei Jiang, Neal Krawetz, Sameer Kumar, David Kunzman, Jonathan Lai, Chee Wai Lee, Julio Maia, Tareq Malas, Ryan McGreevy, Chao Mei, Marcelo Melo, Sarah Moe, Mark Nelson, James Phillips, Brian Radak, Joao Ribeiro, Till Rudack, Osman Sarood, Aritomo Shinozaki, Mohammad Soroush Barhaghi, David Tanner, Josh Vermaas, Peng Wang, Yi Wang, David Wells, Ke Yue, Gengbin Zheng, Fangqiang Zhu


June 15, 2024






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

Description

The NAMD User's 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 development is supported by National Institutes of Health grants NIH P41-GM104601 and NIH R24-GM145965.

NAMD Version 3.0

Authors: Rafael Bernardi, Milind Bhandarkar, Abhinav Bhatele, Eric Bohm, W. Michael Brown, Robert Brunner, Ronak Buch, Floris Buelens, Haochuan Chen, Christophe Chipot, Jaemin Choi, Han-Yi Chou, David Clark, Andrew Dalke, Surjit Dixit, Giacomo Fiorin, Peter Freddolino, Haohao Fu, Paul Grayson, Justin Gullingsrud, Attila Gursoy, David Hardy, Chris Harrison, Jerome Hénin, William Humphrey, David Hurwitz, Antti-Pekka Hynninen, Barry Isralewitz, Nikhil Jain, Wei Jiang, Neal Krawetz, Sameer Kumar, David Kunzman, Jonathan Lai, Chee Wai Lee, Julio Maia, Tareq Malas, Ryan McGreevy, Chao Mei, Marcelo Melo, Sarah Moe, Mark Nelson, James Phillips, Brian Radak, Joao Ribeiro, Till Rudack, Osman Sarood, Aritomo Shinozaki, Mohammad Soroush Barhaghi, David Tanner, Josh Vermaas, Peng Wang, Yi Wang, David Wells, Ke Yue, Gengbin Zheng, Fangqiang Zhu

Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois.

©1995-2023 The Board of Trustees of the University of Illinois. All Rights Reserved