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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. | 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 Overview== | ||
Revision as of 13:20, 22 July 2021
Navigation: Documentation / Overview
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 |