What is NAMD, and where is it installed at IU and on XSEDE?

Nanoscale Molecular Dynamics (NAMD) is scalable parallel molecular dynamics application based on Charm++ parallel objects. NAMD is designed for high-performance simulations of large biomolecular systems. NAMD was developed by the Theoretical and Computational Biophysics Group (TCBG) in the Beckman Institute for Advanced Science and Technology at the University of Illinois, Urbana-Champaign (UIUC). For more, see the NAMD website and the NAMD User's Guide.

At Indiana University, NAMD is available on the Big Red II, Karst, and Mason research computing systems.

Mason, Indiana University's large memory computer cluster, will be retired on January 1, 2018. For more, see About the Mason retirement.

If you need help using NAMD on an IU research computing system, email the UITS Scientific Applications and Performance Tuning (SciAPT) team.

For more information about the availability of software on the Indiana University shared central systems, see At IU, what software is available on the research computing systems?

To determine which Extreme Science and Engineering Discovery Environment (XSEDE) digital services have this application installed, use the XSEDE User Portal Software Search. Enter the application name in the Search software box. As you type, search results (i.e., systems with that application installed) are returned automatically. To list all available applications, leave the Search software box empty, and then sort the results by digital service (click Resources), category (click Science Category/Domain), or Service Provider (click Sites).

Similarly, to determine whether an XSEDE Science Gateway provides access to this application, use the search tool on the Gateway Applications page in the XSEDE User Portal.

If this application is not listed, most likely it is not installed on any XSEDE digital services nor accessible from any XSEDE Science Gateways. If a scientific application that is integral to your research is not available, or if a necessary module associated with an installed package is not available, contact the XSEDE Help Desk to request its installation.

If you need help using NAMD on an XSEDE digital system or have questions, contact the XSEDE Help Desk.

This document was developed with support from National Science Foundation (NSF) grants 1053575 and 1548562. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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Last modified on 2017-07-19 08:45:20.

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