RedMD--reduced molecular dynamics package
2009 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 30(2009), 14 vom: 15. Nov., Seite 2364-73 |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2009
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Nucleic Acids Proteins |
| Zusammenfassung: | 2009 Wiley Periodicals, Inc. We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one-bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared-memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/ |
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| Beschreibung: | Date Completed 19.01.2010 Date Revised 31.08.2009 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.21223 |