Category:Biased molecular dynamics - Revision history

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

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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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Huebsch at 09:37, 24 April 2023

2023-04-24T09:37:25Z

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Huebsch at 14:40, 7 April 2022

2022-04-07T14:40:01Z

← Older revision		Revision as of 14:40, 7 April 2022
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	----		----

	[[Category:VASP\|Constrained molecular dynamics]][[Category:Molecular ~~Dynamics~~]]		[[Category:VASP\|Constrained molecular dynamics]][[Category:Molecular dynamics]]

Karsai: Created page with "== Theory == Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. == How to == Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. ---- Category:VASP..."

2019-03-13T13:52:40Z

Created page with "== Theory == *Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. == How to == *Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. ---- Category:VASP..."

New page

== Theory ==
*Biased molecular dynamics: {{TAG|Biased molecular dynamics}}.

== How to ==
*Biased molecular dynamics: {{TAG|Biased molecular dynamics}}.

----

[[Category:VASP|Constrained molecular dynamics]][[Category:Molecular Dynamics]]

Category:Biased molecular dynamics - Revision history

Huebsch at 13:06, 28 February 2025

Csheldon: /* Related methods in VASP */

Karsai at 10:07, 15 October 2024

Huebsch: /* Output */

Huebsch: /* Output */

Huebsch: (move edit by Karsai to main)

Huebsch at 09:37, 24 April 2023

Huebsch at 14:40, 7 April 2022

Karsai: Created page with "== Theory == *Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. == How to == *Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. ---- Category:VASP..."

Karsai: Created page with "== Theory == Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. == How to == Biased molecular dynamics: {{TAG|Biased molecular dynamics}}. ---- Category:VASP..."