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

被引:80
作者
Biarnes, Xevi [1 ,4 ]
Pietrucci, Fabio [2 ]
Marinelli, Fabrizio [3 ]
Laio, Alessandro [4 ]
机构
[1] IQS, Lab Biochem, ES-08017 Barcelona, Spain
[2] Ecole Polytech Fed Lausanne, CECAM, CH-1015 Lausanne, Switzerland
[3] Max Planck Inst Biophys MPIBP, DE-60438 Frankfurt, Germany
[4] SISSA, IT-34136 Trieste, Italy
关键词
Metadynamics; Bias exchange; VMD; PLUMED; Molecular dynamics simulation; Thermodynamics; Kinetics; FREE-ENERGY CALCULATIONS;
D O I
10.1016/j.cpc.2011.08.020
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
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).
引用
收藏
页码:203 / 211
页数:9
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