Overview: Difference between revisions

From PMFLib Wiki
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 2: Line 2:
----
----
__NOEDITSECTION__
__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. 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==


Line 9: Line 7:
! Method
! Method
! Abbreviation
! Abbreviation
! ∆G
! ∆A
! ∆H
! ∆U
! -T∆S
! -T∆S
! Multiple-Walkers Approach
! MWA*
! Comment
! Comment
|-
|-
Line 21: Line 19:
| Y
| Y
| Y
| Y
| including US-ABF (Umbrella Sampling)
|-
|-
| [[Adaptive Biasing Potential Method]]
| [[Adaptive Biasing Potential Method]]
Line 28: Line 27:
| N
| N
| Y
| Y
|
|  
|-
|-
| [[Constrained Dynamics]]
| [[Constrained Dynamics]]
Line 37: Line 36:
| N
| N
|
|
|-
| [[Restrained Dynamics]]
| RST
| Y
| N
| N
| N
| US (Umbrella Sampling) via WHAM
|-
|-
| [[Metadynamics]]
| [[Metadynamics]]
Line 44: Line 51:
| 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==
Line 64: Line 91:
! 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
Line 84: Line 111:
| [https://cats.ncbr.muni.cz CATs]
| [https://cats.ncbr.muni.cz CATs]
|  
|  
|-
| 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
Retrieved from "https://pmflib.ncbr.muni.cz/wiki6/index.php?title=Overview&oldid=578"