About: PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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. 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. (en)
Title	PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS (en)
skos:prefLabel	PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS (en)
skos:notation	RIV/00216224:14740/11:00050024!RIV12-GA0-14740___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GD301/09/H004), P(LC06030), Z(MSM0021622413)
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Kulhánek, Petr Střelcová, Zora Koča, Jaroslav
http://linked.open.../riv/druhVysledku	O - Ostatní výsledky nezařaditelné do žádného z výše uvedených druhů výsledku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	220633
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/11:00050024
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	free energy; potential of mean force (en)
http://linked.open.../riv/klicoveSlovo	free energy potential of mean force
http://linked.open...ontrolniKodProRIV	[C43FD74F0AE3]
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Molecular and structural biology of selected antitumor drugs. From mechanistic studies to chemotherapy of tumors Biomolecular centre
http://linked.open...UplatneniVysledku	2011
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Kulhánek, Petr Střelcová, Zora Fuxreiter, Monika Mones, Letif Simon, Istvan
http://linked.open...n/vavai/riv/zamer	Proteiny v metabolismu a při interakci organismů s prostředím
http://localhost/t...ganizacniJednotka	14740

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