Metadynamics calculations - Revision history

Csheldon at 15:07, 28 May 2026

2026-05-28T15:07:17Z

← Older revision		Revision as of 15:07, 28 May 2026
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	#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file		#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file

	The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>[[Metadynamics~~\|Metadynamics]]~~</tt>.		The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.

	<div id="BiasedMD"></div>		<div id="BiasedMD"></div>

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

2026-05-28T15:02:53Z

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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	#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file		#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file

	The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.		The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>[[Metadynamics\|Metadynamics]]</tt>.

	=== Nose-Hoover thermostat ===		=== Nose-Hoover thermostat ===
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	#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file		#If needed, define the bias potential in the {{FILE\|PENALTYPOT}}-file

	The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.		The actual time-dependent bias potential is written to the {{FILE\|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE\|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE\|HILLSPOT}} to {{FILE\|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE\|REPORT}}-file, check the lines after the string <tt>[[Metadynamics\|Metadynamics]]</tt>.

	<div id="BiasedMD"></div>		<div id="BiasedMD"></div>

Csheldon at 13:39, 28 May 2026

2026-05-28T13:39:57Z

← Older revision		Revision as of 13:39, 28 May 2026
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	<div id="BiasedMD"></div>		<div id="BiasedMD"></div>


	== Related tags and sections ==		== Related tags and sections ==

Csheldon at 13:39, 28 May 2026

2026-05-28T13:39:40Z

← Older revision		Revision as of 13:39, 28 May 2026
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	<div id="BiasedMD"></div>		<div id="BiasedMD"></div>


	== Related tags and sections ==		== Related tags and sections ==
			{{FILE\|ICONST}}, {{TAG\|HILLS_H}}, {{TAG\|HILLS_W}}, {{TAG\|HILLS_BIN}}, {{FILE\|PENALTYPOT}}, {{FILE\|HILLSPOT}}, {{FILE\|REPORT}}

	[[Metadynamics]], [[Nuclephile_Substitution_CH3Cl_-_mMD3 \| Nucleophilic substitution of chloromethane by chloride using metadynamics]]		[[Metadynamics]], [[Nuclephile_Substitution_CH3Cl_-_mMD3 \| Nucleophilic substitution of chloromethane by chloride using metadynamics]]

Csheldon at 13:00, 10 February 2026

2026-02-10T13:00:20Z

← Older revision		Revision as of 13:00, 10 February 2026
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	== Related tags and sections ==		== Related tags and sections ==
	[[Metadynamics]]		[[Metadynamics]], [[Nuclephile_Substitution_CH3Cl_-_mMD3 \| Nucleophilic substitution of chloromethane by chloride using metadynamics]]

	<references/>		<references/>

Csheldon at 14:49, 5 November 2024

2024-11-05T14:49:32Z

← Older revision		Revision as of 14:49, 5 November 2024
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	[[Metadynamics]]		[[Metadynamics]]

	~~== References ==~~
	<references/>		<references/>

Csheldon at 14:49, 5 November 2024

2024-11-05T14:49:10Z

← Older revision		Revision as of 14:49, 5 November 2024
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	<div id="BiasedMD"></div>		<div id="BiasedMD"></div>

			== Related tags and sections ==
			[[Metadynamics]]

	== References ==		== References ==

Karsai at 11:55, 16 October 2024

2024-10-16T11:55:51Z

← Older revision		Revision as of 11:55, 16 October 2024
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	~~== How to ==~~

	=== Anderson thermostat ===		=== Anderson thermostat ===

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	----		----

	[[Category:Advanced molecular-dynamics sampling]][[Category:~~How to~~]]		[[Category:Advanced molecular-dynamics sampling]][[Category:Howto]]

Karsai: Created page with " == How to == === Anderson thermostat === * For a metadynamics 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 ({{TAG|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG|ANDERSEN_PROB}} #Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}} #Define collective variables in the {{FILE|ICONST}}-file, and set the `S..."`


2024-10-16T11:55:06Z
Created page with "  == How to ==  === Anderson thermostat ===  * For a metadynamics 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 ({{TAG|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG|ANDERSEN_PROB}} #Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}} #Define collective variables in the {{FILE|ICONST}}-file, and set the <code>S..."
New page




== How to ==



=== Anderson thermostat ===



* For a metadynamics 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 ({{TAG|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}

#Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}}

#Define collective variables in the {{FILE|ICONST}}-file, and set the <code>STATUS</code> parameter for the collective variables to 5

#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file



The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.



=== Nose-Hoover thermostat ===

* For a metadynamics run with Nose-Hoover thermostat, one has to:

#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}

#Set {{TAG|MDALGO}}=2 ({{TAG|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG|SMASS}}

#Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}}

#Define collective variables in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5

#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file



The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.



<div id="BiasedMD"></div>



== References ==

<references/>



<noinclude>

----



[[Category:Advanced molecular-dynamics sampling]][[Category:How to]]