PMFLib Wiki

Overview: Difference between revisions

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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. 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==


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! Method
! Method
! Abbreviation
! Abbreviation
! ∆G
! ∆A
! ∆H
! ∆U
! -T∆S
! -T∆S
! Multiple-Walkers Approach
! MWA*
! Comment
! Comment
|-
|-
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| Y
| Y
| Y
| Y
| including US-ABF (Umbrella Sampling)
|-
|-
| [[Adaptive Biasing Potential Method]]
| [[Adaptive Biasing Potential Method]]
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| N
| N
| Y
| Y
|
|  
|-
|-
| [[Constrained Dynamics]]
| [[Constrained Dynamics]]
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| N
| N
|
|
|-
| [[Restrained Dynamics]]
| RST
| Y
| N
| N
| N
| US (Umbrella Sampling) via WHAM
|-
|-
| [[Metadynamics]]
| [[Metadynamics]]
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| N
| N
| Y
| Y
|
| including well-tempered metadynamics
|-
|-
| [[Umbrella Sampling - Adaptive Biasing Force Method]]
| [[String Method]]
| US-ABF
| STM
| Y
| Y
| Y
| Y
| N
| N
| N
| N
|
|-
! <center>'''Supporting Method'''</center>
! colspan="6" |
|-
| [[Path Driving]]
| PDRV
| colspan="4" |
|
|-
| [[Collective Variable Monitoring]]
| MON
| colspan="4" |
|
|-
| [[Metric Tensor Correction]]
| MTC
| colspan="4" |
|
|
|}
|}
* MWA = Multiple Walker Approach Extension


==Drivers==
==Drivers==
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! Comment
! Comment
|-
|-
| SANDER
| SANDER-DYNAMIC
| sander
| sander.PMF
| 17
| 22, 24
| Y
| Y
| [https://ambermd.org AMBER]
| [https://ambermd.org AMBER]
|  
|  
|-
|-
| PMEMD-NEW
| PMEMD-DYNAMIC
| pmemd
| pmemd.PMF
| 16
| 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]
|  
|  
|-
| PMEMD
| pmemd
|
| Y
| [https://ambermd.org AMBER]
| obsolete, not updated in PMFLib v6.0
|-
| CPMD
| cpmd
|
| Y
| [https://www.cpmd.org CPMD]
| outdated
|-
| CP2K
| cp2k
|
| N
| [https://www.cp2k.org/ CP2K]
| outdated
|-
| XDYNBP
| XDynBP
|
| N
| private
| outdated
|}
|}
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