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 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; Pietrucci, Fabio (2009-10-01). "PLUMED: A portable plugin for free-energy calculations with molecular dynamics". Computer Physics Communications . 180 (10): 1961– 1972. arXiv :0902.0874 Bibcode :2009CoPhC.180.1961B . doi :10.1016/j.cpc.2009.05.011 . ISSN 0010-4655 . S2CID 4852774 . ^ 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. arXiv :1310.0980 Bibcode :2014CoPhC.185..604T . doi :10.1016/j.cpc.2013.09.018 . ISSN 0010-4655 . S2CID 17904052 . ^ 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. Bibcode :2012CoPhC.183..203B . doi :10.1016/j.cpc.2011.08.020 . ISSN 0010-4655 . ^ "PLUMED: Introduction" . www.plumed.org . Retrieved 2019-05-23 .
External links
