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PMFLib - A Toolkit for Free Energy Calculations

PMFLib implements free energy calculation methods employing biased molecular dynamics (MD) simulations. The following methods are available:

  • Adaptive Biasing Force (ABF) and combination of Umbrella Sampling and Adaptive Biasing Force (US-ABF)
  • Constrained Dynamics (CST), also known as Blue Moon
  • Direct and Well-tempered Metadynamics (MTD)
  • Adaptive Biasing Potential (ABP)

Some methods provide mean forces, which need to be integrated to get free energies. PMFLib offers the following integration techniques:

  • Reverse Finite Differences (RDF)
  • Radial Basis Functions (RBF)
  • Gaussian Process Regression (GPR) with hyperparameter optimization

In addition to the free energy, some methods can provide enthalpy and entropy from the same biased MD simulation.

Supplementary methods include:

  • Monitoring of collective variables
  • Restrained Dynamics

Sampling can be improved by Multiple-walker Approach (MWA), which uses server/client architecture with fully asynchronous communications. MWA is available for ABF, ABP, and MTD.

Further details: https://pmflib.ncbr.muni.cz

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