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

Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio

Producció científica: Article en revista indexadaArticleAvaluat per experts

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Resum

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 relative free energies are then computed by a weighted-histogram procedure and the most relevant free energy wells are identified by diagonalization of the rate matrix followed by a commitor analysis. All this procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data. The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics simulations. METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others. The METAGUI source files can be downloaded from the PLUMED web site (http://www.plumed-code. org).

Idioma originalAnglès
Pàgines (de-a)203-211
Nombre de pàgines9
RevistaComputer Physics Communications
Volum183
Número1
DOIs
Estat de la publicacióPublicada - de gen. 2012

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