a 2011

PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

KULHÁNEK, Petr, Letif MONES, Zora STŘELCOVÁ, Istvan SIMON, Monika FUXREITER et. al.

Basic information

Original name

PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

Authors

KULHÁNEK, Petr (203 Czech Republic, belonging to the institution), Letif MONES (348 Hungary), Zora STŘELCOVÁ (203 Czech Republic, belonging to the institution), Istvan SIMON (348 Hungary), Monika FUXREITER (348 Hungary) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution)

Edition

8th Discussions in Structural Molecular Biology, Nové Hrady, Czech Republic, 2011

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10403 Physical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14740/11:00050024

Organization unit

Central European Institute of Technology

Keywords in English

free energy; potential of mean force

Tags

Změněno: 4/4/2012 10:10, Mgr. Nikola Kostlánová, Ph.D.

Abstract

V originále

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.

Links

GD301/09/H004, research and development project
Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny
Investor: Czech Science Foundation
LC06030, research and development project
Name: Biomolekulární centrum
Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre
MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
205872, interní kód MU
Name: Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions (Acronym: POSTBIOMIN)
Investor: European Union, Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions, Capacities