Biased molecular dynamics calculations - Revision history

Csheldon at 15:06, 28 May 2026

2026-05-28T15:06:33Z

← Older revision		Revision as of 15:06, 28 May 2026
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	=== Output ===		=== Output ===
	:The values of all collective variables defined in the {{FILE\|ICONST}} file 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 defined in the {{FILE\|ICONST}} file for each MD step are listed in the {{FILE\|REPORT}} file. Check the lines after the string <tt>Metadynamics</tt>.

	== Examples of usage ==		== Examples of usage ==

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

	== Examples of usage ==		== Examples of usage ==

Csheldon: /* Related tags and articles */

2026-05-28T14:12:44Z

Related tags and articles

← 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]]

	== References ==		== References ==

Csheldon: /* Related tags and articles */

2026-05-28T13:35:07Z

Related tags and articles

← Older revision		Revision as of 13:35, 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}}

	== References ==		== References ==

Csheldon: /* Related tags and articles */

2026-05-28T13:34:43Z

Related tags and articles

← Older revision		Revision as of 13:34, 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}}, {{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 ==

Csheldon: /* Related tags and articles */

2026-05-28T13:33:53Z

Related tags and articles

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

Csheldon: /* Related methods in VASP */

2026-05-28T13:30:53Z

Related methods in VASP

← Older revision		Revision as of 13:30, 28 May 2026
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	*[[Interface pinning]]: This employs a bias potential to pin the state of an interface between a solid and a liquid. This method uses entirely different {{TAG\|INCAR}} tags than the bias potentials presented on this page.		*[[Interface pinning]]: This employs a bias potential to pin the state of an interface between a solid and a liquid. This method uses entirely different {{TAG\|INCAR}} tags than the bias potentials presented on this page.

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

	== References ==		== References ==

Liebetreu: Reverted edits by Liebetreu (talk) to last revision by Karsai

2026-04-15T12:40:14Z

Reverted edits by Liebetreu (talk) to last revision by Karsai

← Older revision		Revision as of 12:40, 15 April 2026
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	:A sum of Gauss functions (curve (b) in Fig.1)		:A sum of Gauss functions (curve (b) in Fig.1)
	::<math>		::<math>
	\tilde{V}(\xi_1,\dots,\xi_{M}) = \sum_{\nu=1}^{N_5}h_{\nu}\text{exp}\left[ -\frac{\sum_{\mu=1}^{M_5}(\xi_{\mu}(q)-\xi_{0\nu,\mu})^2}{2w_{\nu}^2} \right],</math>		\tilde{V}(\xi_1,\dots,\xi_{M}) = \sum_{\nu=1}^{N_5}h_{\nu}\text{exp}\left [-\frac{\sum_{\mu=1}^{M_5}(\xi_{\mu}(q)-\xi_{0\nu,\mu})^2}{2w_{\nu}^2} \right ], \;
			</math>
	:where <math>N_5</math> is the number of Gaussian functions and <math>M_5</math> is the number of coordinates the potential acts upon. The potential is chosen in the {{FILE\|ICONST}} file by setting the <code>status</code> to 5. The parameters of the potentials, <math>h_{\nu}</math>, <math>w_{\nu}</math>, and <math>\xi_{0\nu,\mu}</math> are defined in the {{FILE\|PENALTYPOT}} file.		:where <math>N_5</math> is the number of Gaussian functions and <math>M_5</math> is the number of coordinates the potential acts upon. The potential is chosen in the {{FILE\|ICONST}} file by setting the <code>status</code> to 5. The parameters of the potentials, <math>h_{\nu}</math>, <math>w_{\nu}</math>, and <math>\xi_{0\nu,\mu}</math> are defined in the {{FILE\|PENALTYPOT}} file.

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	== Examples of usage ==		== Examples of usage ==
	Let us consider the nucleophile substitution reaction of <~~chem~~>~~CH3Cl~~</~~chem~~> with <~~chem~~>Cl-</~~chem~~>. The reactant is a weak van-der-Waals complex. The corresponding {{FILE\|POSCAR}} file reads		Let us consider the nucleophile substitution reaction of CH<math>_3</math>Cl with Cl<math>^-</math>. The reactant is a weak van-der-Waals complex. The corresponding {{FILE\|POSCAR}} file reads

	vdW complex CH3Cl...Cl		vdW complex CH3Cl...Cl
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	6.84157897 6.18713289 4.46842049		6.84157897 6.18713289 4.46842049

	Due to the weak interactions between <~~chem~~>~~CH3Cl~~</~~chem~~> and <~~chem~~>Cl-</~~chem~~>, the complex can collapse at high temperatures. This can be avoided by setting an upper bound for the length of the non-bonding Cl...C interactions.		Due to the weak interactions between CH<math>_3</math>Cl and Cl<math>^-</math>, the complex can collapse at high temperatures. This can be avoided by setting an upper bound for the length of the non-bonding Cl...C interactions.
	This can be conveniently achieved by using a Fermi-like step-shaped bias potential. To this end, we need to define the Cl...C distance, i.e., the distance between the atoms 1 and 5, as a coordinate with status 4 in the {{FILE\|ICONST}} file:		This can be conveniently achieved by using a Fermi-like step-shaped bias potential. To this end, we need to define the Cl...C distance, i.e., the distance between the atoms 1 and 5, as a coordinate with status 4 in the {{FILE\|ICONST}} file:

Liebetreu: /* Gaussian potential */

2026-04-14T10:48:21Z

Gaussian potential

← Older revision		Revision as of 10:48, 14 April 2026
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	:A sum of Gauss functions (curve (b) in Fig.1)		:A sum of Gauss functions (curve (b) in Fig.1)
	::<math>		::<math>
	\tilde{V}(\xi_1,\dots,\xi_{M}) = \sum_{\nu=1}^{N_5}h_{\nu}\text{exp}\left [-\frac{\sum_{\mu=1}^{M_5}(\xi_{\mu}(q)-\xi_{0\nu,\mu})^2}{2w_{\nu}^2} \right ], \;		\tilde{V}(\xi_1,\dots,\xi_{M}) = \sum_{\nu=1}^{N_5}h_{\nu}\text{exp}\left[ -\frac{\sum_{\mu=1}^{M_5}(\xi_{\mu}(q)-\xi_{0\nu,\mu})^2}{2w_{\nu}^2} \right],</math>
	</math>
	:where <math>N_5</math> is the number of Gaussian functions and <math>M_5</math> is the number of coordinates the potential acts upon. The potential is chosen in the {{FILE\|ICONST}} file by setting the <code>status</code> to 5. The parameters of the potentials, <math>h_{\nu}</math>, <math>w_{\nu}</math>, and <math>\xi_{0\nu,\mu}</math> are defined in the {{FILE\|PENALTYPOT}} file.		:where <math>N_5</math> is the number of Gaussian functions and <math>M_5</math> is the number of coordinates the potential acts upon. The potential is chosen in the {{FILE\|ICONST}} file by setting the <code>status</code> to 5. The parameters of the potentials, <math>h_{\nu}</math>, <math>w_{\nu}</math>, and <math>\xi_{0\nu,\mu}</math> are defined in the {{FILE\|PENALTYPOT}} file.

Liebetreu: /* Examples of usage */

2026-04-14T10:45:54Z

Examples of usage

← Older revision		Revision as of 10:45, 14 April 2026
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	== Examples of usage ==		== Examples of usage ==
	Let us consider the nucleophile substitution reaction of CH<~~math~~>_3</~~math~~>Cl with Cl<~~math~~>^-</~~math~~>. The reactant is a weak van-der-Waals complex. The corresponding {{FILE\|POSCAR}} file reads		Let us consider the nucleophile substitution reaction of <chem>CH3Cl</chem> with <chem>Cl-</chem>. The reactant is a weak van-der-Waals complex. The corresponding {{FILE\|POSCAR}} file reads

	vdW complex CH3Cl...Cl		vdW complex CH3Cl...Cl
Line 72:		Line 72:
	6.84157897 6.18713289 4.46842049		6.84157897 6.18713289 4.46842049

	Due to the weak interactions between CH<~~math~~>_3</~~math~~>Cl and Cl<~~math~~>^-</~~math~~>, the complex can collapse at high temperatures. This can be avoided by setting an upper bound for the length of the non-bonding Cl...C interactions.		Due to the weak interactions between <chem>CH3Cl</chem> and <chem>Cl-</chem>, the complex can collapse at high temperatures. This can be avoided by setting an upper bound for the length of the non-bonding Cl...C interactions.
	This can be conveniently achieved by using a Fermi-like step-shaped bias potential. To this end, we need to define the Cl...C distance, i.e., the distance between the atoms 1 and 5, as a coordinate with status 4 in the {{FILE\|ICONST}} file:		This can be conveniently achieved by using a Fermi-like step-shaped bias potential. To this end, we need to define the Cl...C distance, i.e., the distance between the atoms 1 and 5, as a coordinate with status 4 in the {{FILE\|ICONST}} file: