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.
'''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 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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| N
| N
| Y
| Y
|
| including well-tempered metadynamics
|-
|-
| [[Umbrella Sampling - Adaptive Biasing Force Method]]
| [[Umbrella Sampling - Adaptive Biasing Force Method]]
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| Y
| Y
| N
| N
|
|-
| [[String Method]]
| STM
| Y
| N
| N
| N
|
|-
! <center>'''Supporting Method'''</center>
! colspan="6" |
|-
| [[Collective Variable Monitoring]]
| MON
| colspan="4" |
|
|-
| [[Path Driving]]
| PDRV
| colspan="4" |
|
|-
| [[Restrained Dynamics]]
| RST
| colspan="4" |
|
|
|}
|}
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! Driver
! Driver
! Program
! Program
! Compatible Versions
! Parallel execution
! Package
! Package
! Comment
! Comment
|-
|-
| SANDER
| SANDER-DYNAMIC
| sander
| sander.PMF
| 22, 24
| Y
| [https://ambermd.org AMBER]
| [https://ambermd.org AMBER]
|  
|  
|-
|-
| PMEMD-NEW
| PMEMD-DYNAMIC
| pmemd
| pmemd.PMF
| 22, 24
| Y
| [https://ambermd.org AMBER]
| [https://ambermd.org AMBER]
|
| support GPU acceleration
|-
|-
| CATS
| CATS
| cats
| cats
| git master, rolling versioning
| N
| [https://cats.ncbr.muni.cz CATs]
| [https://cats.ncbr.muni.cz CATs]
|  
|  
|-
| PMEMD
| pmemd
| [https://ambermd.org AMBER]
| obsolete, not updated in PMFLib v6.0
|}
|}

Latest revision as of 07:26, 28 May 2025

Navigation: Documentation / Overview

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 the Installation section.

Method Overview

Method Abbreviation ∆G ∆H -T∆S MWA 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 including well-tempered metadynamics
Umbrella Sampling - Adaptive Biasing Force Method US-ABF Y Y Y N
String Method STM Y N N N
Supporting Method
Collective Variable Monitoring MON
Path Driving PDRV
Restrained Dynamics RST

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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