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PMFLib is a toolkit | '''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 Overview== | ||
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! ∆H | ! ∆H | ||
! -T∆S | ! -T∆S | ||
! | ! MWA | ||
! Comment | ! Comment | ||
|- | |- | ||
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| N | | N | ||
| Y | | Y | ||
| | | including well-tempered metadynamics | ||
|- | |- | ||
| [[Umbrella Sampling - Adaptive Biasing Force Method]] | | [[Umbrella Sampling - Adaptive Biasing Force Method]] | ||
| Line 52: | Line 54: | ||
| Y | | Y | ||
| N | | N | ||
| | |||
|- | |||
| [[String Method]] | |||
| STM | |||
| Y | |||
| N | |||
| N | |||
| N | |||
| | |||
|- | |||
! <center>'''Supporting Method'''</center> | |||
! colspan="6" | | |||
|- | |||
| [[Collective Variable Monitoring]] | |||
| MON | |||
| colspan="4" | | |||
| | |||
|- | |||
| [[Path Driving]] | |||
| PDRV | |||
| colspan="4" | | |||
| | |||
|- | |||
| [[Restrained Dynamics]] | |||
| RST | |||
| colspan="4" | | |||
| | | | ||
|} | |} | ||
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! Comment | ! Comment | ||
|- | |- | ||
| SANDER | | SANDER-DYNAMIC | ||
| sander.PMF | | sander.PMF | ||
| | | 22, 24 | ||
| Y | | Y | ||
| [https://ambermd.org AMBER] | | [https://ambermd.org AMBER] | ||
| | | | ||
|- | |- | ||
| PMEMD- | | PMEMD-DYNAMIC | ||
| pmemd.PMF | | pmemd.PMF | ||
| | | 22, 24 | ||
| Y | | Y | ||
| [https://ambermd.org AMBER] | | [https://ambermd.org AMBER] | ||
| | | support GPU acceleration | ||
|- | |- | ||
| CATS | | CATS | ||
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| [https://cats.ncbr.muni.cz CATs] | | [https://cats.ncbr.muni.cz CATs] | ||
| | | | ||
|} | |} | ||
Latest revision as of 07:26, 28 May 2025
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 | ∆G | ∆H | -T∆S | MWA | 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 | including well-tempered metadynamics |
| Umbrella Sampling - Adaptive Biasing Force Method | US-ABF | Y | Y | Y | N | |
| String Method | STM | Y | N | N | N | |
| Collective Variable Monitoring | MON | |||||
| Path Driving | PDRV | |||||
| Restrained Dynamics | RST | |||||
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 |