Submitted by site admin on Fri, 2007-02-09 21:47.
Web Address
and References
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http://www.gromacs.org
- D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and
H. J. C. Berendsen. "GROMACS: Fast, flexible, and free." J. Comput.
Chem., 26, 1701-1718 (2005).
http://dx.doi.org/10.1002/jcc.20291
- E. Lindahl, B. Hess and D. van der Spoel. "GROMACS 3.0: a package for molecular simulation and trajectory analysis." Journal of Molecular Modeling, 7, 306-317 (2001).
http://www.springerlink.com/content/r894b1jx35la6eja
- H. J. C. Berendsen, D. van der Spoel and R. van Drunen. "GROMACS: A
message-passing parallel molecular dynamics implementation." Comput.
Phys. Commun., 91, 43-56 (1995).
http://dx.doi.org/10.1016/0010-4655(95)00042-E
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Related Codes
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User Demographics
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Thousands of users, there are 1200 people on the user mailing list.
Breakdown between academic and industrial users: 90/10
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| Availability |
open source (GPL); development funded by research grants and university salaries
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MD or MC?
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MD. MC is under development.
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Visualization
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limited trajectory viewers; trajectories readable by VMD
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Ensembles
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NPT, NVT, i.e. canonical ensembles
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Force Fields
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GROMOS87, GROMOS96, OPLS-AA/L, Amber 96/99
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Thermostats/
Barostats
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Thermostats: Berendsen, Nose-Hoover
Barostats: Berendsen, Parrinello-Rahman
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NEMD?
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Special visocosity calculations, constant acceleration of arbitrary subsets of the system, electric fields
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Parallel
Capabilities
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see http://www.gromacs.org/benchmarks
This is currently under heavy development. |
Long-Range
Interactions
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PME
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Distinguishing
Characteristics
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Flexibility, speed, features, analysis tools
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Analysis
Routines
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Many, specifically aimed at protein simulation but also at molecular physics, e.g. transport properties, dielectric properties etc.
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