Overview

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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	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Obsolete or Outdated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CPMD	cpmd.PMF		Y	CPMD	outdated
CP2K	cp2k.PMF		N	CP2K	outdated
XDYNBP	XDynBP		N	private	outdated