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Manuscript Title: METAGUI. A VMD Interface for Analyzing Metadynamics and Molecular Dynamics Simulations.
Authors: Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio
Program title: METAGUI
Catalogue identifier: AEKH_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 183(2012)203
Programming language: TK/TCL, Fortran.
Computer: Any computer with a VMD installation and capable of running an executable produced by a gfortran compiler.
Operating system: Linux, Unix OS-es.
RAM: 1073741824 bytes
Keywords: Metadynamics, VMD, PLUMED, Molecular Dynamics Simulation, Thermodynamics, Kinetics.
Classification: 23.

External routines: A VMD installation (http://www.ks.uiuc.edu/Research/vmd/)

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.

Solution method:
Graphical-user interface linked to VMD that
  1. clusterizes the simulation trajectories in the space of a set of collective variables and assigns each frame to a given microstate,
  2. determines the free energy of each microstate by a weighted histogram analysis method, and
  3. identifies the most relevant free energy wells (kinetic basins) by diagonalization of the rate matrix followed by a commitor analysis.

Restrictions:
Input format files compatible with PLUMED and all the MD engines suported by PLUMED and VMD

Running time:
A few minutes