Overview

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PMFLib is a toolkit, which implements several methods for free energy calculations employing biased molecular dynamics (MD) simulations. While PMFLib provides its own molecular dynamics engine, PMFLib usage is rather oriented on coupling with other well-established and optimized molecular dynamics simulations programs. The reference MD code is sander from the AMBER package. The code is free-ware, and thus, its source code coupled with PMFLib is available for download. The compilation is simple and described in the Installation section.

Method Overview

Method Abbreviation ∆G ∆H -T∆S Multiple-Walkers Approach Comment
Adaptive Biasing Force Method ABF Y Y Y Y
Adaptive Biasing Potential Method ABP Y N N Y
Constrained Dynamics CST Y Y Y N
Metadynamics MTD Y N N Y
Umbrella Sampling - Adaptive Biasing Force Method US-ABF Y Y Y N

Drivers

Driver Program Package Comment
SANDER sander AMBER
PMEMD-NEW pmemd AMBER
CATS cats CATs
PMEMD pmemd AMBER obsolete, not updated in PMFLib v6.0