Software:PLUMED
| Developer(s) | Max Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth Tribello |
|---|---|
| Initial release | 2009 |
| Stable release | 2.7.1
/ April 16, 2021 |
| Repository | github |
| Written in | C++ (bindings also available for C, Fortran, and Python) |
| Operating system | Linux, macOS |
| Type | Molecular dynamics |
| License | GNU LGPL |
| Website | www |
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used to together with analysis and visualization tools VMD, HTMD, and OpenPathSampling.[1][2]
In addition, PLUMED can be used as a standalone tool for analysis of molecular dynamics trajectories. A graphical user interface named METAGUI is available.[3]
Collective variables
PLUMED offers a large collection of collective variables that serve as descriptions of complex processes that occur during molecular dynamics simulations, for example angles, positions, distances, interaction energies, and total energy.[4]
References
- ↑ Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni; Camilloni, Carlo; Provasi, Davide; Raiteri, Paolo; Donadio, Davide; Marinelli, Fabrizio et al. (2009-10-01). "PLUMED: A portable plugin for free-energy calculations with molecular dynamics". Computer Physics Communications 180 (10): 1961–1972. doi:10.1016/j.cpc.2009.05.011. ISSN 0010-4655. Bibcode: 2009CoPhC.180.1961B.
- ↑ Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni (2014-02-01). "PLUMED 2: New feathers for an old bird". Computer Physics Communications 185 (2): 604–613. doi:10.1016/j.cpc.2013.09.018. ISSN 0010-4655. Bibcode: 2014CoPhC.185..604T.
- ↑ Biarnés, Xevi; Pietrucci, Fabio; Marinelli, Fabrizio; Laio, Alessandro (2012-01-01). "METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations". Computer Physics Communications 183 (1): 203–211. doi:10.1016/j.cpc.2011.08.020. ISSN 0010-4655. Bibcode: 2012CoPhC.183..203B.
- ↑ "PLUMED: Introduction". https://www.plumed.org/doc-master/user-doc/html/index.html.
External links
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