PLUMED 2: New feathers for an old bird

Published: 1 February 2014| Version 1 | DOI: 10.17632/sy5zfpb9w6.1
Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible... Title of program: PLUMED 2 Catalogue Id: AEEE_v2_0 Nature of problem Calculation of free-energy surfaces for molecular systems of interest in biology, chemistry and materials science, on the fly and a-posteriori analysis of molecular dynamics trajectories using advanced collective variables Versions of this program held in the CPC repository in Mendeley Data AEEE_v1_0; PLUMED; 10.1016/j.cpc.2009.05.011 AEEE_v2_0; PLUMED 2; 10.1016/j.cpc.2013.09.018



Molecular Biology, Surface Science, Condensed Matter Physics, Statistical Physics, Biological Sciences, Computational Physics, Thermodynamics