METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Published: 1 January 2012| Version 1 | DOI: 10.17632/8gr322zpgb.1
Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially designed for analyzing metadynamics based simulations. The huge amount of diverse structures generated during such a simulation is partitioned into a set of microstates (i.e. structures with similar values of the collective variables). Their re... Title of program: METAGUI Catalogue Id: AEKH_v1_0 Nature of problem Extract thermodynamic data and build a kinetic model of a given process simulated by metadynamics or molecular dynamics simulations, and provide this information on a dual representation that allows navigating and exploring the molecular structures corresponding to each point along the multidimensional free energy hypersurface. Versions of this program held in the CPC repository in Mendeley Data AEKH_v1_0; METAGUI; 10.1016/j.cpc.2011.08.020



Statistical Physics, Computational Physics, Thermodynamics