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
This package can be build:
- independently
- as an extension of sander