PMFLib Wiki pmfwiki6 https://pmflib.ncbr.muni.cz/wiki6/index.php/Documentation MediaWiki 1.44.2 first-letter Media Special Talk User User talk pmflibwiki pmflibwiki talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 4 586 577 2026-05-30T17:17:31Z Kulhanek 1 586 wikitext text/x-wiki __NOTOC__ __NOEDITSECTION__ PMFLib is a versatile toolkit for calculating free energy profiles in molecular systems using methods based on biased molecular dynamics (MD) simulations. It provides a flexible framework for defining collective variables, applying biasing techniques, collecting sampling data, and reconstructing free energy surfaces. PMFLib implements several established methods for free energy calculations, including the Adaptive Biasing Force method and its umbrella-sampling variant, the Adaptive Biasing Potential method, Constrained Dynamics, Restrained Dynamics, Metadynamics including its well-tempered variant, and the String Method. Free energy calculations can be further accelerated using the Multiple Walker approach, which is implemented through an asynchronous client/server architecture. For selected methods, PMFLib also supports decomposition of the free energy into internal energy and entropic contributions, providing additional insight into the thermodynamic origin of the calculated profiles. Although PMFLib includes its own molecular dynamics engine, its main purpose is to work as an extension to established and highly optimized external MD programs. In this mode, PMFLib controls the biasing protocol and evaluates collective variables, while the external MD engine performs the actual propagation of the molecular system. The reference external engines are sander and pmemd from the AMBER package, for which PMFLib provides integrated interfaces. * Reference manual ** [[Overview]] ** [[Control file]] *** [[Collective Variables]] *** [[Paths]] *** [[Methods]] ** [[Utilities]] ** [[Technical Details]] * [[Tutorials]] * [[Installation]] * [[References]] 4fj3370j2hiq33ttkqmtbp3gubfqxni