PLUMED

Last updated
PLUMED
Developers Max Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth Tribello
Initial release2009;16 years ago (2009)
Stable release
2.9.3 / January 21, 2025;11 months ago (2025-01-21)
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

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]

Contents

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

  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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