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

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).Program summaryProgram title: METAGUICatalogue identifier: AEKH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKH_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: GNU General Public License version 3No. of lines in distributed program, including test data, etc.: 117 545No. of bytes in distributed program, including test data, etc.: 8 516 203Distribution format: tar.gzProgramming language: TK/TCL, FortranComputer: Any computer with a VMD installation and capable of running an executable produced by a gfortran compilerOperating system: Linux, Unix OS-esRAM: 1 073 741 824 bytesClassification: 23External 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 multi-dimensional free energy hypersurface.Solution method: Graphical-user interface linked to VMD that1.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, and3.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 supported by PLUMED and VMD.Running time: A few minutes.