PLUMED: A portable plugin for free-energy calculations with molecular dynamics

By Massimiliano Bonomi, D. Branduardi, Giovanni Bussi, Carlo Camilloni, D. Provasi, P. Raiteri, Davide Donadio, F. Marinelli, F. Pietrucci, R. Broglia and 1 more. Computer Physics Communications, 2009

1,723 citations recorded by the source corpus.

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes.

Subfields: Atomic and Molecular Physics, and Optics, Condensed Matter Physics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/26832a6e6f7cebcfde48ee4b698afba87692da3b

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In Atomic and Molecular Physics, and Optics

In Condensed Matter Physics

In Molecular Biology

Citations in the corpus

Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “Variationally enhanced sampling is implemented in the VES Code module of PLUMED 2.”
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013, methodology): “A major help in this regard is the PLUMED package [243,244], which patches a variety of MD codes to enable users to use many of the techniques discussed here.”
From sequence to Boltzmann weighted ensemble of structures with AlphaFold2-RAVE (2022, methodology): “We used PLUMED 2.4 26–28 to extract collective variables.”
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. (2009, methodology): “ACEMD also provides a scripting interface to control and program the molecular dynamics run to perform complex protocols like umbrella sampling, steered molecular dynamics and sheared boundary conditions and metadynamics simulations 27 .”
Effect of moisture on the mechanical properties of CFRP–wood composite: An experimental and atomistic investigation (2015, methodology): “The determination of the FEP is performed using the metadynamics method [55] in the PLUMED package [56].”