Biased molecular dynamics - Revision history

Csheldon at 08:09, 9 June 2026

2026-06-09T08:09:15Z

← Older revision		Revision as of 08:09, 9 June 2026
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	<references/>		<references/>

	[[Category:Advanced molecular-dynamics sampling]][[Category:Theory]]		[[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Theory]]

Csheldon at 15:07, 28 May 2026

2026-05-28T15:07:36Z

← Older revision		Revision as of 15:07, 28 May 2026
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	#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.		#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.

	The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string Metadynamics.		The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.

	== Related tags and articles ==		== Related tags and articles ==

Csheldon at 15:06, 28 May 2026

2026-05-28T15:06:57Z

← Older revision		Revision as of 15:06, 28 May 2026
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	#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.		#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.

	The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string ~~<tt>[[~~Metadynamics~~\|Metadynamics]]</tt>~~.		The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string Metadynamics.

	== Related tags and articles ==		== Related tags and articles ==

Csheldon: Sprint 164: add cross-links in running text for advanced MD sampling pages

2026-05-28T15:02:52Z

Sprint 164: add cross-links in running text for advanced MD sampling pages

← Older revision		Revision as of 15:02, 28 May 2026
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	#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.		#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.

	The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.		The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>[[Metadynamics\|Metadynamics]]</tt>.

	== Related tags and articles ==		== Related tags and articles ==

Csheldon: /* Related tags and articles */

2026-05-28T14:12:56Z

Csheldon: /* Related tags and articles */

2026-05-28T13:34:58Z

Csheldon: /* Related tags and articles */

2026-05-28T13:33:47Z

Csheldon at 13:30, 28 May 2026

2026-05-28T13:30:39Z

← Older revision		Revision as of 13:30, 28 May 2026
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	The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.		The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.

			== Related tags and articles ==
			{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{FILE\|REPORT}}

	== References ==		== References ==

Huebsch: /* How to */

2025-10-21T13:14:23Z

How to

← Older revision		Revision as of 13:14, 21 October 2025
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	* For a biased molecular dynamics run with [[Andersen thermostat]], one has to:		* For a biased molecular dynamics run with [[Andersen thermostat]], one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=1 (or {{TAG\|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}.		#Choose thermostat:
			## Set {{TAG\|MDALGO}}=1 (or {{TAG\|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}.
			## Set {{TAG\|MDALGO}}=2 (or {{TAG\|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG\|SMASS}}.
	#In order to avoid updating of the bias potential, set {{TAG\|HILLS_BIN}}={{TAG\|NSW}}.		#In order to avoid updating of the bias potential, set {{TAG\|HILLS_BIN}}={{TAG\|NSW}}.
	#Define collective variables in the {{FILE\|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5.		#Define collective variables in the {{FILE\|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5.
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	The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.		The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.


	== References ==		== References ==

Huebsch at 12:53, 21 October 2025

2025-10-21T12:53:47Z

← Older revision		Revision as of 12:53, 21 October 2025
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	One of the most popular methods using bias potentials is umbrella sampling{{cite\|torrie:jcp:1977}}. This method uses a bias potential to enhance sampling of ξ in regions with low ''P''(ξ<sub>''i''</sub>), e.g., transition regions of chemical reactions. The correct distributions are recovered afterward using the equation for <math>\langle A \rangle_{H}</math> above.		One of the most popular methods using bias potentials is umbrella sampling{{cite\|torrie:jcp:1977}}. This method uses a bias potential to enhance sampling of ξ in regions with low ''P''(ξ<sub>''i''</sub>), e.g., transition regions of chemical reactions. The correct distributions are recovered afterward using the equation for <math>\langle A \rangle_{H}</math> above.

			=== How to ===

			For a description of biased molecular dynamics see {{TAG\|Biased molecular dynamics}}.

			* For a biased molecular dynamics run with [[Andersen thermostat]], one has to:
			#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
			#Set {{TAG\|MDALGO}}=1 (or {{TAG\|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}.
			#In order to avoid updating of the bias potential, set {{TAG\|HILLS_BIN}}={{TAG\|NSW}}.
			#Define collective variables in the {{FILE\|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5.
			#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.

			The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.


	== References ==		== References ==

← Older revision		Revision as of 14:12, 28 May 2026
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	== Related tags and articles ==		== Related tags and articles ==
	{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{TAG\|FBIAS_R0}}, {{TAG\|FBIAS_A}}, {{TAG\|FBIAS_D}}, {{TAG\|SPRING_K}}, {{TAG\|SPRING_R0}}, {{TAG\|SPRING_V0}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{TAG\|FBIAS_R0}}, {{TAG\|FBIAS_A}}, {{TAG\|FBIAS_D}}, {{TAG\|SPRING_K}}, {{TAG\|SPRING_R0}}, {{TAG\|SPRING_V0}}, {{FILE\|REPORT}}

			[[Biased molecular dynamics calculations]]

	== References ==		== References ==

← Older revision		Revision as of 12:53, 21 October 2025
Line 34:		Line 34:

	One of the most popular methods using bias potentials is umbrella sampling{{cite\|torrie:jcp:1977}}. This method uses a bias potential to enhance sampling of ξ in regions with low ''P''(ξ<sub>''i''</sub>), e.g., transition regions of chemical reactions. The correct distributions are recovered afterward using the equation for <math>\langle A \rangle_{H}</math> above.		One of the most popular methods using bias potentials is umbrella sampling{{cite\|torrie:jcp:1977}}. This method uses a bias potential to enhance sampling of ξ in regions with low ''P''(ξ<sub>''i''</sub>), e.g., transition regions of chemical reactions. The correct distributions are recovered afterward using the equation for <math>\langle A \rangle_{H}</math> above.

			=== How to ===

			For a description of biased molecular dynamics see {{TAG\|Biased molecular dynamics}}.

			* For a biased molecular dynamics run with [[Andersen thermostat]], one has to:
			#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
			#Set {{TAG\|MDALGO}}=1 (or {{TAG\|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}.
			#In order to avoid updating of the bias potential, set {{TAG\|HILLS_BIN}}={{TAG\|NSW}}.
			#Define collective variables in the {{FILE\|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5.
			#Define the bias potential in the {{FILE\|PENALTYPOT}} file if necessary.

			The values of all collective variables for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.


	== References ==		== References ==

← Older revision		Revision as of 13:34, 28 May 2026
Line 51:		Line 51:

	== Related tags and articles ==		== Related tags and articles ==
	{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{TAG\|FBIAS_R0}}, {{TAG\|FBIAS_A}}, {{TAG\|FBIAS_D}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{TAG\|FBIAS_R0}}, {{TAG\|FBIAS_A}}, {{TAG\|FBIAS_D}}, {{TAG\|SPRING_K}}, {{TAG\|SPRING_R0}}, {{TAG\|SPRING_V0}}, {{FILE\|REPORT}}

	== References ==		== References ==

← Older revision		Revision as of 13:33, 28 May 2026
Line 51:		Line 51:

	== Related tags and articles ==		== Related tags and articles ==
	{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{FILE\|PENALTYPOT}}, {{TAG\|HILLS_BIN}}, {{TAG\|FBIAS_R0}}, {{TAG\|FBIAS_A}}, {{TAG\|FBIAS_D}}, {{FILE\|REPORT}}

	== References ==		== References ==