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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.
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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| Y
| Y
| Y
| Y
| N
|
|-
| Adaptive Biasing Force Method - testing code
| TABF
| Y
| Y
| Y
| N
|
|-
| [[String Method]]
| STM
| Y
| N
| N
| N
| untested in PMFLib v6
|-
| colspan="7" | <center>'''Supporting Methods'''</center>
|-
| [[Collective Variable Monitoring]]
| MON
| N
| N
| N
| N
|
|-
| [[Path Driving]]
| PDRV
| N
| N
| N
| N
|
|-
| [[Restrained Dynamics]]
| RST
| N
| N
| N
| N
| N
|
|
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|-
|-
| SANDER
| SANDER
| sander
| sander.PMF
| 17
| 17
| Y
| Y
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|-
|-
| PMEMD-NEW
| PMEMD-NEW
| pmemd
| pmemd.PMF
| 16
| 16
| Y
| Y
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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'''Obsolete or Outdated'''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
| pmemd
| pmemd.PMF
|
|
| Y
| Y
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|-
|-
| CPMD
| CPMD
| cpmd
| cpmd.PMF
|  
|  
| Y
| Y
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|-
|-
| CP2K
| CP2K
| cp2k
| cp2k.PMF
|  
|  
| N
| N

Latest revision as of 09:52, 23 July 2021

Navigation: Documentation / Overview


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 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
Adaptive Biasing Force Method - testing code TABF Y Y Y N
String Method STM Y N N N untested in PMFLib v6
Supporting Methods
Collective Variable Monitoring MON N N N N
Path Driving PDRV N N N N
Restrained Dynamics RST N N N N

Drivers

Driver Program Compatible Versions Parallel execution Package Comment
SANDER sander.PMF 17 Y AMBER
PMEMD-NEW pmemd.PMF 16 Y AMBER
CATS cats git master, rolling versioning N CATs
Obsolete or Outdated
PMEMD pmemd.PMF Y AMBER obsolete, not updated in PMFLib v6.0
CPMD cpmd.PMF Y CPMD outdated
CP2K cp2k.PMF N CP2K outdated
XDYNBP XDynBP N private outdated