Category:Biased molecular dynamics - Revision history

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

2026-04-15T12:28:39Z

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

← Older revision		Revision as of 12:28, 15 April 2026
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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: /* Examples of usage */

2026-04-14T13:26:04Z

Examples of usage

← Older revision		Revision as of 13:26, 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

Liebetreu: /* Examples of usage */

2026-04-14T13:25:25Z

Examples of usage

← Older revision		Revision as of 13:25, 14 April 2026
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	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:

Singraber at 21:36, 17 October 2025

2025-10-17T21:36:16Z

← Older revision		Revision as of 21:36, 17 October 2025
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	== How to ==		== How to ==
	*First one needs to setup a [[:Category:Molecular dynamics\|standard molecular dynamics]] run. The bias potentials are supported in both the [[NVT ensemble\|NVT]] and [[NpT ensemble\|NpT]] MD simulations, regardless of the particular [[:Category:Thermostats\|thermostat]] and/or [[PSTRESS\|barostat]] setting.		*First one needs to setup a [[:Category:Molecular dynamics\|standard molecular dynamics]] run. The bias potentials are supported in both the [[NVT ensemble\|NVT]] and [[NpT ensemble\|NpT]] MD simulations, regardless of the particular [[:Category:Thermostats\|thermostat]] and/or [[PSTRESS\|barostat]] setting.
	{{NB\|mind\|Mind that for VASP 5.x the biased molecular dynamics runs have to be chosen by adding 10 to the chosen value of {{TAG\|MDALGO}}. E.g. {{TAG\|MDALGO}}{{=}}12 instead of {{TAG\|MDALGO}}{{=}}2 has to be chosen for ~~Nose~~-Hoover thermostat.\|:}}		{{NB\|mind\|Mind that for VASP 5.x the biased molecular dynamics runs have to be chosen by adding 10 to the chosen value of {{TAG\|MDALGO}}. E.g. {{TAG\|MDALGO}}{{=}}12 instead of {{TAG\|MDALGO}}{{=}}2 has to be chosen for [[Nosé-Hoover thermostat]].\|:}}
	*Then one needs to set the geometric parameters and bias potential types. The geometric parameters ξ, also called collective variables, that are controlled via the potentials are defined in the {{TAG\|ICONST}} file. The type of bias potential is also set in this file. The format of this file follows this layout:		*Then one needs to set the geometric parameters and bias potential types. The geometric parameters ξ, also called collective variables, that are controlled via the potentials are defined in the {{TAG\|ICONST}} file. The type of bias potential is also set in this file. The format of this file follows this layout:
	flag item(1) ... item(N) status		flag item(1) ... item(N) status

Huebsch at 13:06, 28 February 2025

2025-02-28T13:06:20Z

← Older revision		Revision as of 13:06, 28 February 2025
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	<references/>		<references/>

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

Csheldon: /* Related methods in VASP */

2024-10-29T12:37:39Z

Related methods in VASP

← Older revision		Revision as of 12:37, 29 October 2024
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	== Related methods in VASP ==		== Related methods in VASP ==
	*[[~~:Category:Metadynamics\|~~Metadynamics]]: In contrast to the methods discussed on this page metadynamics continuously updates the bias potential of the system to push it into unvisited parts of phase space.		*[[Metadynamics]]: In contrast to the methods discussed on this page metadynamics continuously updates the bias potential of the system to push it into unvisited parts of phase space.

	*[[:Category:Interface pinning\|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.		*[[:Category:Interface pinning\|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.

Karsai at 10:07, 15 October 2024

2024-10-15T10:07:44Z

← Older revision		Revision as of 10:07, 15 October 2024
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	'''Biased molecular dynamics''' (MD) refers to advanced [[:Category:Molecular dynamics\|MD-simulation methods]] that introduce a ''bias potential''. One of the most important purposes of using bias potentials is to enhance the sampling of phase space with low probability density (e.g., transition regions of chemical reactions). Depending on the type of sampling and in combination with the corresponding statistical methods one then has access to important thermodynamic quantities like, e.g., free energies. Biased molecular dynamics comes in very different flavors such as, e.g., umbrella sampling{{cite\|torrie:jcp:1977}} and umbrella integration{{cite\|kaestner:jcp:2005}}, to name a few~~. In the following, a short theoretical overview, an introduction to the available bias potentials, and a description of how to use bias potentials in VASP is given~~. For a comprehensive description (especially about umbrella sampling), we refer the interested user to Ref. {{cite\|frenkel:ap-book:2002}} written by D. Frenkel and B. Smit.		''Biased molecular dynamics''' (MD) refers to advanced [[:Category:Molecular dynamics\|MD-simulation methods]] that introduce a ''bias potential''. One of the most important purposes of using bias potentials is to enhance the sampling of phase space with low probability density (e.g., transition regions of chemical reactions). Depending on the type of sampling and in combination with the corresponding statistical methods one then has access to important thermodynamic quantities like, e.g., free energies. Biased molecular dynamics comes in very different flavors such as, e.g., umbrella sampling{{cite\|torrie:jcp:1977}} and umbrella integration{{cite\|kaestner:jcp:2005}}, to name a few. For a comprehensive description (especially about umbrella sampling), we refer the interested user to Ref. {{cite\|frenkel:ap-book:2002}} written by D. Frenkel and B. Smit.

	~~== Theoretical background ==~~

	The probability density for a geometric parameter ξ of the system driven by a Hamiltonian		The probability density for a geometric parameter ξ of the system driven by a Hamiltonian
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	<references/>		<references/>

	[[Category:~~VASP\|Biased~~ molecular dynamics]][[Category:~~Molecular dynamics~~]]		[[Category:Advanced molecular-dynamics sampling]][[Category:Theory]]

Huebsch: /* Output */

2024-06-14T06:10:12Z

Output

← Older revision	Revision as of 06:10, 14 June 2024
(No difference)

Huebsch: /* Output */

2024-06-14T06:10:12Z

Output

← Older revision		Revision as of 06:10, 14 June 2024
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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</tt>.

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

Huebsch: (move edit by Karsai to main)

2023-10-20T07:57:51Z

(move edit by Karsai to main)

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