String Method - Revision history

Kulhanek at 13:29, 20 June 2026

2026-06-20T13:29:41Z

← Older revision		Revision as of 13:29, 20 June 2026
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	* [[STM:Client]]		* [[STM:Client]]
	** [[STM:Client Controls]]		** [[STM:Client Controls]]
	** [[STM:Collective ~~variables~~]]		** [[STM:Collective Variables]]
	* [[STM:Post-processing]]		* [[STM:Post-processing]]
	* [[STM:Utilities]]		* [[STM:Utilities]]

Kulhanek at 21:54, 2 June 2026

2026-06-02T21:54:34Z

← Older revision		Revision as of 21:54, 2 June 2026
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	* [[STM:Server]]		* [[STM:Server]]
	** [[STM:Server Controls]]		** [[STM:Server Controls]]
			** [[STM:Path]]
	* [[STM:Client]]		* [[STM:Client]]
	** [[STM:Client Controls]]		** [[STM:Client Controls]]

Kulhanek at 21:09, 2 June 2026

2026-06-02T21:09:41Z

← Older revision		Revision as of 21:09, 2 June 2026
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	==Contents==		==Contents==
	* [[STM:Server]]		* [[STM:Server]]
	** [[STM::Server Controls]]		** [[STM:Server Controls]]
	* [[STM:Client]]		* [[STM:Client]]
	** [[STM:Client Controls]]		** [[STM:Client Controls]]

Kulhanek at 18:50, 2 June 2026

2026-06-02T18:50:17Z

← Older revision		Revision as of 18:50, 2 June 2026
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	__NOEDITSECTION__		__NOEDITSECTION__
	=Introduction=		=Introduction=
	The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.		The string method (STM) is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	[[Image:MTC-STM-d1d2-01.apng\|center]]		[[Image:MTC-STM-d1d2-01.apng\|center]]

Kulhanek at 18:17, 2 June 2026

2026-06-02T18:17:51Z

← Older revision		Revision as of 18:17, 2 June 2026
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	==Contents==		==Contents==
	* [[~~String Method#Description\|~~STM:~~Description~~]]		* [[STM:Server]]
	* [[STM:Controls]]		** [[STM::Server Controls]]
	* [[STM:Collective variables]]		* [[STM:Client]]
			** [[STM:Client Controls]]
			** [[STM:Collective variables]]
	* [[STM:Post-processing]]		* [[STM:Post-processing]]
	* [[STM:Utilities]]		* [[STM:Utilities]]
	* [[STM:Examples]]		* [[STM:Examples]]

	==References==		===References===
	(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. ''J. Chem. Phys.'' '''2006''', ''125 (2)'', 024106. https://doi.org/10.1063/1.2212942.		(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. ''J. Chem. Phys.'' '''2006''', ''125 (2)'', 024106. https://doi.org/10.1063/1.2212942.

Kulhanek at 18:15, 2 June 2026

2026-06-02T18:15:17Z

← Older revision		Revision as of 18:15, 2 June 2026
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	The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.		The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	[[Image:MTC-STM-d1d2-01.apng]]		[[Image:MTC-STM-d1d2-01.apng\|center]]

	PMFLib implements the approach described in the article ''String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces'' [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes, synchronous and asynchronous, enabling effective utilisation of various computational resources.		PMFLib implements the approach described in the article ''String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces'' [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes, synchronous and asynchronous, enabling effective utilisation of various computational resources.

Kulhanek at 18:14, 2 June 2026

2026-06-02T18:14:55Z

← Older revision		Revision as of 18:14, 2 June 2026
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	----		----
	__NOEDITSECTION__		__NOEDITSECTION__
			=Introduction=
			The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

			[[Image:MTC-STM-d1d2-01.apng]]

			PMFLib implements the approach described in the article ''String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces'' [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes, synchronous and asynchronous, enabling effective utilisation of various computational resources.

	==Contents==		==Contents==
	* [[String Method#Description\|STM:Description]]		* [[String Method#Description\|STM:Description]]
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	* [[STM:Utilities]]		* [[STM:Utilities]]
	* [[STM:Examples]]		* [[STM:Examples]]


	~~==Introduction==~~
	The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more metastable states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	~~[[Image:MTC-STM-d1d2-01.apng]]~~

	PMFLib implements the approach described in the article ''String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces'' [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes: synchronous and asynchronous, enabling effective utilisation of various computational resources.

	==References==		==References==
	(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. ''J. Chem. Phys.'' '''2006''', ''125 (2)'', 024106. https://doi.org/10.1063/1.2212942.		(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. ''J. Chem. Phys.'' '''2006''', ''125 (2)'', 024106. https://doi.org/10.1063/1.2212942.

Kulhanek at 18:12, 2 June 2026

2026-06-02T18:12:43Z

← Older revision		Revision as of 18:12, 2 June 2026
Line 12:		Line 12:

	==Introduction==		==Introduction==
	The string method is an enhanced sampling technique ~~to identify~~ the most probable transition pathway (minimum free energy path) between two or more metastable states in high-dimensional collective variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.		The string method is an enhanced sampling technique for identifying the most probable transition pathway (minimum free-energy path) between two or more metastable states in high-dimensional collective-variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	[[Image:MTC-STM-d1d2-01.apng]]		[[Image:MTC-STM-d1d2-01.apng]]

			PMFLib implements the approach described in the article ''String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces'' [1] with many improvements. The path is described using splines (interpolating or smoothing) and optimised with advanced gradient-based algorithms such as ADM (Adaptive Moment Estimation) and its variants. Technically, the implementation uses a client/server architecture and operates in two modes: synchronous and asynchronous, enabling effective utilisation of various computational resources.

			==References==
			(1) Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces. ''J. Chem. Phys.'' '''2006''', ''125 (2)'', 024106. https://doi.org/10.1063/1.2212942.

Kulhanek at 18:00, 2 June 2026

2026-06-02T18:00:19Z

← Older revision		Revision as of 18:00, 2 June 2026
Line 14:		Line 14:
	The string method is an enhanced sampling technique to identify the most probable transition pathway (minimum free energy path) between two or more metastable states in high-dimensional collective variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.		The string method is an enhanced sampling technique to identify the most probable transition pathway (minimum free energy path) between two or more metastable states in high-dimensional collective variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	[[Image:~~Movie~~.~~png~~]]		[[Image:MTC-STM-d1d2-01.apng]]

Kulhanek at 15:03, 2 June 2026

2026-06-02T15:03:46Z

← Older revision		Revision as of 15:03, 2 June 2026
Line 14:		Line 14:
	The string method is an enhanced sampling technique to identify the most probable transition pathway (minimum free energy path) between two or more metastable states in high-dimensional collective variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.		The string method is an enhanced sampling technique to identify the most probable transition pathway (minimum free energy path) between two or more metastable states in high-dimensional collective variable space. The method discretises the path into a series of connected points (beads) and iteratively refines their positions using biased molecular dynamics to align the path with the underlying free energy landscape.

	[[Image:Movie.png~~\|1000px~~]]		[[Image:Movie.png]]