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.
|Titolo:||PLUMED: A portable plugin for free-energy calculations with molecular dynamics|
|Autori:||Bonomi M; Branduardi D; Bussi G; Camilloni C; Provasi D; Raiteri P; Donadio D; Marinelli F; Pietrucci F; Broglia RA; Parrinello M|
|Data di pubblicazione:||2009|
|Digital Object Identifier (DOI):||10.1016/j.cpc.2009.05.011|
|Appare nelle tipologie:||1.1 Journal article|