Prof. Alessandro Laio
Statistical and Biological Physics
Trieste, Italy

Tuesday, April 2, 2013
9:30 am (CT)
3269 Beckman Institute

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 long-scale molecular dynamics. The tool is specially designed for analyising metadynamics based simulations. The huge ammount of diverse structures generated during such a simulation are grouped together into a set of microstates (i.e. structures with similar values of the collective variables). Their relative free energies are then computed by a wheighted-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 trajectories. METAGUI is based on the output format of the PLUMED 1.3 plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others.