Overview: Difference between revisions

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PMFLib is a toolkit that implements several free energy calculations methods 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 direct 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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|
|
|-
|-
| [[Metadynamics]]
| [[Restrained Dynamics]]
| MTD
| RST
| Y
| Y
| N
| N
| N
| N
| Y
| N
|
| US (Umbrella Sampling) via WHAM
|-
|-
| [[Umbrella Sampling - Adaptive Biasing Force Method]]
| [[Metadynamics]]
| US-ABF
| MTD
| Y
| Y
| Y
| Y
| N
| N
|
| N
|-
| Adaptive Biasing Force Method - testing code
| TABF
| Y
| Y
| Y
| Y
| N
| including well-tempered metadynamics
|
|-
|-
| [[String Method]]
| [[String Method]]
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| N
| N
| N
| N
| untested in PMFLib v6
|  
|-
|-
| colspan="7" | <center>'''Supporting Methods'''</center>
! <center>'''Supporting Method'''</center>
! colspan="6" |
|-
| [[Path Driving]]
| PDRV
| colspan="4" |
|
|-
|-
| [[Collective Variable Monitoring]]
| [[Collective Variable Monitoring]]
| MON
| MON
| N
| colspan="4" |  
| N
| N
| N
|
|
|-
|-
| [[Path Driving]]
| [[Metric Tensor Correction]]
| PDRV
| MTC
| N
| colspan="4" |  
| N
| N
| N
|
|-
| [[Restrained Dynamics]]
| RST
| N
| N
| N
| N
|
|
|}
|}
* MWA = Multiple Walker Approach Extension


==Drivers==
==Drivers==
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! Comment
! Comment
|-
|-
| SANDER
| SANDER-DYNAMIC
| sander.PMF
| sander.PMF
| 17
| 22, 24
| Y
| Y
| [https://ambermd.org AMBER]
| [https://ambermd.org AMBER]
|  
|  
|-
|-
| PMEMD-NEW
| PMEMD-DYNAMIC
| pmemd.PMF
| 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]
|  
|  
|-
| colspan="6" | <center>'''Obsolete or Outdated'''</center>
|-
| PMEMD
| pmemd.PMF
|
| Y
| [https://ambermd.org AMBER]
| obsolete, not updated in PMFLib v6.0
|-
| CPMD
| cpmd.PMF
|
| Y
| [https://www.cpmd.org CPMD]
| outdated
|-
| CP2K
| cp2k.PMF
|
| N
| [https://www.cp2k.org/ CP2K]
| outdated
|-
| XDYNBP
| XDynBP
|
| N
| private
| outdated
|}
|}

Latest revision as of 16:07, 30 May 2026

Navigation: Documentation / Overview

Method Overview

Method Abbreviation ∆A ∆U -T∆S MWA* Comment
Adaptive Biasing Force Method ABF Y Y Y Y including US-ABF (Umbrella Sampling)
Adaptive Biasing Potential Method ABP Y N N Y
Constrained Dynamics CST Y Y Y N
Restrained Dynamics RST Y N N N US (Umbrella Sampling) via WHAM
Metadynamics MTD Y N N Y including well-tempered metadynamics
String Method STM Y N N N
Supporting Method
Path Driving PDRV
Collective Variable Monitoring MON
Metric Tensor Correction MTC
  • MWA = Multiple Walker Approach Extension

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
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