English
PMFLib is a set of programs and libraries suited for free energy calculations by means of the potential of mean force methods (PMF). It currently implements the following PMF methods:
- the adaptive biasing force method (ABF)
- the constrained dynamics (CON, also known as Blue Moon)
- metadynamics (MTD)
- restrained dynamics (RST)
- the string method (STM)
The sampling can be improved by the multiple walkers approach (MWA) in conjunction with the adaptive biasing force method and metadynamics. The library implements advanced collective variables (reaction coordinates) allowing to calculate multidimensional free energy surfaces.
How to cite
If your work is based on data obtanined by PMFLib, please, use the reference shown below. It is also necessary to cite articles describing individual methods, see Documentation for their summary.
- Kulhánek, P.; Bouchal, T.; Durník, I.; Štěpán, J.; Fuxreiter, M.; Mones, L.; Petřek, M.; Střelcová, Z. PMFLib - A Toolkit for Free Energy Calculations; https://pmflib.ncbr.muni.cz, 2018.