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Navigation: [[Documentation]] / [[Overview]] | Navigation: [[Documentation]] / [[Overview]] | ||
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PMFLib is a toolkit, which implements several methods for free energy calculations employing biased molecular dynamics simulations. While PMFLib provides its own molecular dynamics engine, | __NOEDITSECTION__ | ||
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. | |||
==Method Overview== | ==Method Overview== | ||
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==Drivers== | ==Drivers== | ||
{| class="wikitable" | |||
! Driver | |||
! Program | |||
! Package | |||
! Comment | |||
|- | |||
| SANDER | |||
| sander | |||
| [https://ambermd.org AMBER] | |||
| | |||
|- | |||
| PMEMD-NEW | |||
| pmemd | |||
| [https://ambermd.org AMBER] | |||
| | |||
|- | |||
| CATS | |||
| cats | |||
| [https://cats.ncbr.muni.cz CATs] | |||
| | |||
|- | |||
| PMEMD | |||
| pmemd | |||
| [https://ambermd.org AMBER] | |||
| obsolete, not updated in PMFLib v6.0 | |||
|} | |||
Revision as of 13:02, 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.
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 |