Slow-growth approach - Revision history

Csheldon at 14:10, 28 May 2026

2026-05-28T14:10:34Z

← Older revision		Revision as of 14:10, 28 May 2026
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	{{FILE\|ICONST}}, {{TAG\|INCREM}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{TAG\|INCREM}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}

	[[~~Constrained molecular dynamics~~]]		[[Slow-growth approach calculations]]

	== References ==		== References ==

Csheldon at 14:09, 28 May 2026

2026-05-28T14:09:47Z

← Older revision		Revision as of 14:09, 28 May 2026
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	== Related tags and articles ==		== Related tags and articles ==
	{{FILE\|ICONST}}, {{TAG\|INCREM}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{TAG\|INCREM}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}

			[[Constrained molecular dynamics]]

	== References ==		== References ==

Csheldon at 14:00, 28 May 2026

2026-05-28T14:00:12Z

← Older revision		Revision as of 14:00, 28 May 2026
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	== Related tags and articles ==		== Related tags and articles ==
	{{FILE\|ICONST}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}		{{FILE\|ICONST}}, {{TAG\|INCREM}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}

	== References ==		== References ==

	~~----~~

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

Csheldon at 13:57, 28 May 2026

2026-05-28T13:57:43Z

← Older revision		Revision as of 13:57, 28 May 2026
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	The free-energy profile along a geometric parameter <math>\xi</math> can be scanned by an approximate slow-growth		The free-energy profile along a geometric parameter <math>\xi</math> can be scanned by an approximate slow-growth
	approach~~<ref name="woo1997"/>~~.		approach{{Cite\|woo:ziegler:1997}}.
	In this method, the value of <math>\xi</math> is linearly changed		In this method, the value of <math>\xi</math> is linearly changed
	from the value characteristic for the initial state (1) to that for		from the value characteristic for the initial state (1) to that for
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	corresponds to the free-energy difference between the the final and initial state.		corresponds to the free-energy difference between the the final and initial state.
	In the general case, <math>w^{irrev}_{1 \rightarrow 2}</math> is the irreversible work related		In the general case, <math>w^{irrev}_{1 \rightarrow 2}</math> is the irreversible work related
	to the free energy via Jarzynski's identity~~<ref name="jarzynski1997"/>~~:		to the free energy via Jarzynski's identity {{Cite\|jarzynski:prl:1997}}:

	::<math>		::<math>
Line 27:		Line 27:
	transformation.		transformation.
	Detailed description of the simulation protocol that employs Jarzynski's identity		Detailed description of the simulation protocol that employs Jarzynski's identity
	can be found in reference ~~<ref name="oberhofer2005"/>~~.		can be found in reference {{Cite\|overhofer:geissler:2005}}.

	== How to ==		== How to ==
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	</ol>		</ol>

			== Related tags and articles ==
			{{FILE\|ICONST}}, {{TAG\|SHAKEMAXITER}}, {{TAG\|SHAKETOL}}, {{TAG\|SHAKETOLSOFT}}, {{TAG\|LBLUEOUT}}, {{FILE\|REPORT}}

	== References ==		== References ==
	~~<references>~~
	~~<ref name="woo1997">[https://pubs.acs.org/doi/abs/10.1021/jp9717296 T. K. Woo, P. M. Margl, P. E. Blochl, and T. Ziegler, J. Phys. Chem. B 101, 7877 (1997).]</ref>~~
	~~<ref name="jarzynski1997">[https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.78.2690 C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).]</ref>~~
	~~<ref name="oberhofer2005">[https://pubs.acs.org/doi/abs/10.1021/jp044556a . Oberhofer, C. Dellago, and P. L. Geissler, J. Phys. Chem. B 109, 6902 (2005).]</ref>~~
	~~</references>~~
	----		----

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

Huebsch at 13:10, 21 October 2025

2025-10-21T13:10:37Z

← Older revision		Revision as of 13:10, 21 October 2025
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	* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:		* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
	#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, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Choose a thermostat:
			## Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			## Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}
	#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

Huebsch at 12:46, 21 October 2025

2025-10-21T12:46:21Z

← Older revision		Revision as of 12:46, 21 October 2025
Line 28:		Line 28:
	Detailed description of the simulation protocol that employs Jarzynski's identity		Detailed description of the simulation protocol that employs Jarzynski's identity
	can be found in reference <ref name="oberhofer2005"/>.		can be found in reference <ref name="oberhofer2005"/>.

			== How to ==
			* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
			#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
			#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
			#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

			<ol start="5">
			<li>Specify the transformation velocity-related {{TAG\|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt>.</li>
			</ol>

Karsai at 13:54, 16 October 2024

2024-10-16T13:54:53Z

@@ Line 29: / Line 29: @@
 can be found in reference <ref name="oberhofer2005"/>.
 == References ==
@@ Line 62: / Line 38: @@
 ----
-[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]
+[[Category:Advanced molecular-dynamics sampling]][[Category:Theory]]

Huebsch: /* Anderson thermostat */

2024-06-14T06:12:07Z

Anderson thermostat

← Older revision		Revision as of 06:12, 14 June 2024
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	#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, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
	#Define geometric constraints in the {{FILE\|ICONST}}-file, and set the ~~{{TAG\|~~STATUS}} parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the '''STATUS''' parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

Singraber at 10:27, 16 November 2023

2023-11-16T10:27:20Z

← Older revision		Revision as of 10:27, 16 November 2023
Line 14:		Line 14:
	In the limit of infinitesimally small <math>\dot{\xi}</math>, the work <math>w^{irrev}_{1 \rightarrow 2}</math>		In the limit of infinitesimally small <math>\dot{\xi}</math>, the work <math>w^{irrev}_{1 \rightarrow 2}</math>
	corresponds to the free-energy difference between the the final and initial state.		corresponds to the free-energy difference between the the final and initial state.
	In the general case, <math>w^{irrev}_{1 \rightarrow 2}$ </math>is the irreversible work related		In the general case, <math>w^{irrev}_{1 \rightarrow 2}</math> is the irreversible work related
	to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:		to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:

Ftran at 08:34, 20 October 2023

2023-10-20T08:34:17Z

← Older revision		Revision as of 08:34, 20 October 2023
Line 61:		Line 61:
	</references>		</references>
	----		----
	~~[[The_VASP_Manual\|Contents]]~~

	[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]

← Older revision		Revision as of 13:10, 21 October 2025
Line 32:		Line 32:
	* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:		* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
	#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, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Choose a thermostat:
			## Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			## Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}
	#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

← Older revision		Revision as of 06:12, 14 June 2024
Line 34:		Line 34:
	#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, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
	#Define geometric constraints in the {{FILE\|ICONST}}-file, and set the ~~{{TAG\|~~STATUS}} parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the '''STATUS''' parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.