Name
Title | ||
|---|---|---|
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. |
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 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). |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1016/j.cpc.2011.08.020 | Computer Physics Communications |
Keywords | Field | DocType |
Metadynamics,Bias exchange,VMD,PLUMED,Molecular dynamics simulation,Thermodynamics,Kinetics | Mathematical optimization,Metadynamics,Computer science,Matrix (mathematics),Collective variables,Theoretical computer science,Ministate,Kinetic model,Graphical user interface,Computational science,Molecular dynamics,Plug-in | Journal |
Volume | Issue | ISSN |
183 | 1 | 0010-4655 |
Citations | PageRank | References |
6 | 0.86 | 4 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Xevi Biarnés | 1 | 7 | 1.23 |
| Fabio Pietrucci | 2 | 82 | 7.71 |
| Fabrizio Marinelli | 3 | 258 | 20.55 |
| Alessandro Laio | 4 | 41 | 10.47 |