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PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

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KULHÁNEK Petr MONES Letif STŘELCOVÁ Zora SIMON Istvan FUXREITER Monika KOČA Jaroslav

Rok publikování 2011
Druh Konferenční abstrakty
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
Popis 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.
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