PLUMED

PLUMED
Developer(s)	Max Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth Tribello
Initial release	2009; 15 years ago
Stable release	2.7.1 / April 16, 2021; 3 years ago
Repository	github.com/plumed/plumed2
Written in	C++ (bindings also available for C, Fortran, and Python)
Operating system	Linux, macOS
Type	Molecular dynamics
License	GNU LGPL
Website	www.plumed.org

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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

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[1] 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.

[2] 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.

[3] 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.

[4] "PLUMED: Introduction". www.plumed.org. Retrieved 2019-05-23.

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