Overview
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PMFLib is a toolkit that implements several free energy calculations methods 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 direct 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 | |
| Adaptive Biasing Force Method - testing code | TABF | Y | Y | Y | N | |
| String Method | STM | Y | N | N | N | untested in PMFLib v6 |
| Collective Variable Monitoring | MON | N | N | N | N | |
| Path Driving | PDRV | N | N | N | N | |
| Restrained Dynamics | RST | N | N | N | N | |
Drivers
| Driver | Program | Compatible Versions | Parallel execution | Package | Comment |
|---|---|---|---|---|---|
| SANDER | sander.PMF | 17 | Y | AMBER | |
| PMEMD-NEW | pmemd.PMF | 16 | Y | AMBER | |
| CATS | cats | git master, rolling versioning | N | CATs | |
| PMEMD | pmemd.PMF | Y | AMBER | obsolete, not updated in PMFLib v6.0 | |
| CPMD | cpmd.PMF | Y | CPMD | outdated | |
| CP2K | cp2k.PMF | N | CP2K | outdated | |
| XDYNBP | XDynBP | N | private | outdated | |