Adelaide Research & Scholarship
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https://hdl.handle.net/2440/63253
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| Type: | Journal article |
| Title: | TNAMD: Implementation of TIGER2 in NAMD |
| Author: | Menz, W. Penna, M. Biggs, M. |
| Citation: | Computer Physics Communications, 2010; 181(12):2082-2085 |
| Publisher: | Elsevier Science BV |
| Issue Date: | 2010 |
| ISSN: | 0010-4655 1879-2944 |
| Statement of Responsibility: | William J. Menz, Matthew J. Penna, Mark J. Biggs |
| Abstract: | Replica-exchange molecular dynamics (REMD) must be used to enhance sampling when there are significant (relative to kT) barriers between different parts of the phase space. TIGER2 is a next-generation REMD method that offers more efficient sampling compared to the original REMD method by reducing the number of replicas required to span a given temperature range. In this paper, we present an implementation of the TIGER2 algorithm in the NAMD software package. This implementation exploits the capacity of NAMD to interpret Tcl scripts. The Tcl script implementing TIGER2 is provided and explained in detail, and demonstrated for alanine dipeptide in water. © 2010 Elsevier B.V. All rights reserved. |
| Keywords: | Molecular dynamics Replica-exchange molecular dynamics NAMD TIGER2 method Tool command language Free energy prediction |
| Rights: | Copyright © 2010 Elsevier B.V. All rights reserved. |
| DOI: | 10.1016/j.cpc.2010.09.011 |
| Published version: | http://dx.doi.org/10.1016/j.cpc.2010.09.011 |
| Appears in Collections: | Aurora harvest 5 Chemical Engineering publications Environment Institute publications |
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