View Item 

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

Access Status
Open access
Authors
Bonomi, M.
Branduardi, D.
Bussi, G.
Camilloni, C.
Provasi, D.
Raiteri, Paolo
Donadio, D.
Marinelli, F.
Pietrucci, F.
Broglia, R.
Parrinello, M.
Date
2009
Type
Journal Article

Metadata
Show full item record
Citation
Bonomi, Massimiliano and Branduardi, Davide and Bussi, Giovanni and Camilloni, Carlo and Provasi, Davide and Raiteri, Paolo and Donadio, Davide and Marinelli, Fabrizio and Pietrucci, Fabio and Broglia, Ricardo and Parrinello, Michele. 2009. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications. 180 (10): pp. 1961-1972.
Source Title
Computer Physics Communications
DOI
ISSN
Faculty
Department of Applied Chemistry
Nanochemistry Research Institute (Research Institute)
School of Science
Faculty of Science and Engineering
Remarks

Copyright © 2009 Elsevier B.V. All rights reserved.

URI
Collection
Abstract

Here we present a program aimed at free-energy calculations in molecular systems. It consists of aseries 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. Freeenergy 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.