PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

Kulhánek,  Petr; Mones, Letif; Střelcová,  Zora; Simon, Istvan; Fuxreiter, Monika; Koča,  Jaroslav

PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

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Authors	KULHÁNEK Petr MONES Letif STŘELCOVÁ Zora SIMON Istvan FUXREITER Monika KOČA Jaroslav
Year of publication	2011
Type	Conference abstract
MU Faculty or unit	Central European Institute of Technology
Citation
Description	The majority of chemical and biochemical processes can be described by underlying free energy behavior. One of the most commonly used simulation technique providing the free energy is the calculation of potential of mean force (PMF). PMF represents the free energy along a prescribed reaction coordinate and thus provides information about kinetics and thermodynamics of the studied (bio)chemical events. We have implemented five well established PMF methods into a single suite of programs, which we call PMFLib. Implemented methods are as follows: adaptive biasing force, constrained dynamics, metadynamics, umbrella sampling, and string method. Currently, interfaces to AMBER, CPMD, and XdynBP molecular dynamics codes are available. PMFLib also offers multiple-walkers extension of MTD and ABF methods. Another implemented method improving sampling is replica-exchange molecular dynamics.This allows utilization of PMFLib in calculations employing massive parallel simulations in heterogeneous computer environments.
Related projects:	Proteins in metabolism and interaction of organisms with the environment Biomolecular centre Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions Molekulární a strukturní biologie vybraných cytostatik. Od mechanických studií k chemoterapii rakoviny