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Overview (view source)

Revision as of 07:24, 28 May 2025

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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.
'''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 detail in the [[Installation]] section.


==Method Overview==
==Method Overview==
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! ∆H
! ∆H
! -T∆S
! -T∆S
! Multiple-Walkers Approach
! MWA
! Comment
! Comment
|-
|-
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| [[Umbrella Sampling - Adaptive Biasing Force Method]]
| [[Umbrella Sampling - Adaptive Biasing Force Method]]
| US-ABF
| US-ABF
| Y
| Y
| Y
| N
|
|-
| Adaptive Biasing Force Method - testing code
| TABF
| Y
| Y
| Y
| Y
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| N
| N
| N
| N
| untested in PMFLib v6
|  
|-
|-
| colspan="7" | <center>'''Supporting Methods'''</center>
! <center>'''Supporting Method'''</center>
! colspan="6" |
|-
|-
| [[Collective Variable Monitoring]]
| [[Collective Variable Monitoring]]
| MON
| MON
| N
| colspan="4" |  
| N
| N
| N
|
|
|-
|-
| [[Path Driving]]
| [[Path Driving]]
| PDRV
| PDRV
| N
| colspan="4" |  
| N
|
| N
| N
|  
|-
|-
| [[Restrained Dynamics]]
| [[Restrained Dynamics]]
| RST
| RST
| N
| colspan="4" |  
| N
| N
| N
|
|
|}
|}
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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
|}
|}
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