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Revision as of 15:53, 30 May 2026
Navigation: Documentation / Overview
PMFLib is a versatile toolkit for performing free energy calculations using various methods based on biased molecular dynamics (MD) simulations. Although PMFLib includes its own MD engine, it is primarily designed to interface with well-established and optimized external MD software. The reference MD engine is sander from the AMBER package.
PMFLib is distributed as free software, and its source code—along with the integrated MD interface—is available for direct download. The compilation process is straightforward and is described in the Installation section.
Method Overview
| Method | Abbreviation | ∆A | ∆U | -T∆S | MWA | Comment |
|---|---|---|---|---|---|---|
| Adaptive Biasing Force Method | ABF | Y | Y | Y | Y | including US-ABF |
| Adaptive Biasing Potential Method | ABP | Y | N | N | Y | |
| Constrained Dynamics | CST | Y | Y | Y | N | |
| Restrained Dynamics | RST | |||||
| Metadynamics | MTD | Y | N | N | Y | including well-tempered metadynamics |
| String Method | STM | Y | N | N | N | |
| Path Driving | PDRV | |||||
| Collective Variable Monitoring | MON | |||||
| Metric Tensor Correction | MTC | |||||
Drivers
| Driver | Program | Compatible Versions | Parallel execution | Package | Comment |
|---|---|---|---|---|---|
| SANDER-DYNAMIC | sander.PMF | 22, 24 | Y | AMBER | |
| PMEMD-DYNAMIC | pmemd.PMF | 22, 24 | Y | AMBER | support GPU acceleration |
| CATS | cats | git master, rolling versioning | N | CATs |