Category:Transition states - Revision history

Csheldon: /* Additional resources */

2026-03-24T13:50:51Z

Additional resources

← Older revision		Revision as of 13:50, 24 March 2026
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	=== Books and lectures ===		=== Books and lectures ===
	*''Investigating chemical reactions with VASP - A practical guide'' by Tomáš Bučko - a book guiding modeling chemical reactions in VASP {{Cite\|bucko:book:2025}}.		*''Investigating chemical reactions with VASP - A practical guide'' by Tomáš Bučko - a book guiding modeling chemical reactions in VASP {{Cite\|bucko:book:2025}}.
	*Lecture on modeling chemical reactions (and transition states) using ~~[https~~:~~//youtu.be/mLK7CtDmw0A~~ static approaches].		*Lecture on modeling chemical reactions (and transition states) using {{Video\|static:tomas:2025\|static approaches}}.
	*Lecture on modeling chemical reactions (and transition states) using ~~[https~~:~~//youtu.be/Rk0S-yvxFUo~~ dynamic approaches].		*Lecture on modeling chemical reactions (and transition states) using {{Video\|dynamic:tomas:2025\|dynamic approaches}}.
	*Lecture on modeling chemical reactions (and transition states) using ~~[https~~:~~//youtu.be/bzzHpTBwxbA)~~ machine-learned force fields].		*Lecture on modeling chemical reactions (and transition states) using {{Video\|chem_mlff:ferenc:2025\|machine-learned force fields}}.

	=== Tutorials ===		=== Tutorials ===
	*Tutorial for ~~[https~~:~~//vasp.at/tutorials/latest/transition_states/~~part1/ NEB, IDM, elbow plot, and IRC calculations].		*Tutorial for {{Tutorial\|transition_states:part1\|NEB, IDM, elbow plot, and IRC calculations}}.
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using ~~[https~~:~~//vasp.at/tutorials/latest/transition_states/~~part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using {{Tutorial\|transition_states:part2\|static methods}}.
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using ~~[https~~:~~//vasp.at/tutorials/latest/transition_states/~~part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using {{Tutorial\|transition_states:part3\|dynamic methods}}.
	*Tutorial for ~~[https~~:~~//www.vasp.at/tutorials/latest/md/~~part3~~/#MD-e08~~ dynamic methods for chloromethane-chloride inversion].		*Tutorial for {{Tutorial\|md:part3\|dynamic methods for chloromethane-chloride inversion}}.
	<!--=== How to ===		<!--=== How to ===
	*How to for [[Using_metadynamics_to_train_a_machine-learned_force_field \| training a machine-learned force field (MLFF) using metadynamics for chloromethane-chloride inversion]].-->		*How to for [[Using_metadynamics_to_train_a_machine-learned_force_field \| training a machine-learned force field (MLFF) using metadynamics for chloromethane-chloride inversion]].-->

Csheldon: /* Additional resources */

2026-02-10T13:04:28Z

Additional resources

← Older revision		Revision as of 13:04, 10 February 2026
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	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].
	*Tutorial for [https://www.vasp.at/tutorials/latest/md/part3/#MD-e08 dynamic methods for chloromethane-chloride inversion].		*Tutorial for [https://www.vasp.at/tutorials/latest/md/part3/#MD-e08 dynamic methods for chloromethane-chloride inversion].
	<!--=== How to's ===		<!--=== How to ===
	*How to for [[Using_metadynamics_to_train_a_machine-learned_force_field \| training a machine-learned force field (MLFF) using metadynamics for chloromethane-chloride inversion]].-->		*How to for [[Using_metadynamics_to_train_a_machine-learned_force_field \| training a machine-learned force field (MLFF) using metadynamics for chloromethane-chloride inversion]].-->

Csheldon: /* Tutorials */

2026-02-10T13:03:42Z

Tutorials

← Older revision		Revision as of 13:03, 10 February 2026
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	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].
	*Tutorial for [https://www.vasp.at/tutorials/latest/md/part3/#MD-e08 dynamic methods for chloromethane-chloride inversion].		*Tutorial for [https://www.vasp.at/tutorials/latest/md/part3/#MD-e08 dynamic methods for chloromethane-chloride inversion].
			<!--=== How to's ===
			*How to for [[Using_metadynamics_to_train_a_machine-learned_force_field \| training a machine-learned force field (MLFF) using metadynamics for chloromethane-chloride inversion]].-->

	== References ==		== References ==

	[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]		[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]

Csheldon at 09:17, 12 January 2026

2026-01-12T09:17:49Z

← Older revision		Revision as of 09:17, 12 January 2026
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	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].
	*Tutorial for [https://www.vasp.at/tutorials/latest/md/~~par32~~/#MD-e08 dynamic methods for chloromethane-chloride inversion].		*Tutorial for [https://www.vasp.at/tutorials/latest/md/part3/#MD-e08 dynamic methods for chloromethane-chloride inversion].

	== References ==		== References ==

	[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]		[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]

Csheldon at 09:07, 12 January 2026

2026-01-12T09:07:52Z

← Older revision		Revision as of 09:07, 12 January 2026
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	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].
	~~<!--~~*Tutorial for [https://www.vasp.at/tutorials/latest/md/par32/#MD-e08 dynamic methods for chloromethane-chloride inversion].~~-->~~		*Tutorial for [https://www.vasp.at/tutorials/latest/md/par32/#MD-e08 dynamic methods for chloromethane-chloride inversion].

	== References ==		== References ==

	[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]		[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]

Csheldon: /* Tutorials */

2025-12-11T11:12:11Z

Tutorials

← Older revision		Revision as of 11:12, 11 December 2025
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	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].
			<!--*Tutorial for [https://www.vasp.at/tutorials/latest/md/par32/#MD-e08 dynamic methods for chloromethane-chloride inversion].-->

	== References ==		== References ==

	[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]		[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]

Csheldon: /* Books and lectures */

2025-09-22T10:24:02Z

Books and lectures

← Older revision		Revision as of 10:24, 22 September 2025
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	== Additional resources ==		== Additional resources ==
	=== Books and lectures ===		=== Books and lectures ===
	*"Investigating chemical reactions with VASP - A practical guide" by Tomáš Bučko - a book guiding modeling chemical reactions in VASP {{Cite\|bucko:book:2025}}.		*''Investigating chemical reactions with VASP - A practical guide'' by Tomáš Bučko - a book guiding modeling chemical reactions in VASP {{Cite\|bucko:book:2025}}.
	*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches].		*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches].
	*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/Rk0S-yvxFUo dynamic approaches].		*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/Rk0S-yvxFUo dynamic approaches].

Csheldon: /* Books and lectures */

2025-09-22T10:23:49Z

Books and lectures

← Older revision		Revision as of 10:23, 22 September 2025
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	== Additional resources ==		== Additional resources ==
	=== Books and lectures ===		=== Books and lectures ===
	* ~~Tomáš Bučko has written a book,~~ "Investigating chemical reactions with VASP - A practical guide"~~, to guide in~~ modeling chemical reactions in VASP ~~with accompanying~~ {{Cite\|bucko:book:2025}}. ~~There are also lectures available~~ on ~~our YouTube channel for~~ modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches], [https://youtu.be/Rk0S-yvxFUo dynamic approaches], and [https://youtu.be/bzzHpTBwxbA) machine-learned force fields].		*"Investigating chemical reactions with VASP - A practical guide" by Tomáš Bučko - a book guiding modeling chemical reactions in VASP {{Cite\|bucko:book:2025}}.
			*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches].
			*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/Rk0S-yvxFUo dynamic approaches].
			*Lecture on modeling chemical reactions (and transition states) using [https://youtu.be/bzzHpTBwxbA) machine-learned force fields].

	=== Tutorials ===		=== Tutorials ===

Csheldon: /* Additional resources */

2025-07-11T08:17:05Z

Additional resources

← Older revision		Revision as of 08:17, 11 July 2025
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	== Additional resources ==		== Additional resources ==
	=== Books and lectures ===		=== Books and lectures ===
	* Tomáš Bučko has written a book, ~~[https://stella.uniba.sk/texty/PRIF_TB_investigating_chemical_reactions_vasp.pdf~~ Investigating chemical reactions with VASP - A practical guide], to guide in modeling chemical reactions in VASP with accompanying ~~[https~~:~~//doi.org/10.5281/zenodo.14531578 python scripts]~~. There are also lectures available on our YouTube channel for modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches], [https://youtu.be/Rk0S-yvxFUo dynamic approaches], and [https://youtu.be/bzzHpTBwxbA) machine-learned force fields].		* Tomáš Bučko has written a book, "Investigating chemical reactions with VASP - A practical guide", to guide in modeling chemical reactions in VASP with accompanying {{Cite\|bucko:book:2025}}. There are also lectures available on our YouTube channel for modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches], [https://youtu.be/Rk0S-yvxFUo dynamic approaches], and [https://youtu.be/bzzHpTBwxbA) machine-learned force fields].

	=== Tutorials ===		=== Tutorials ===
	*Tutorial for [https://vasp.at/tutorials/latest/transition_states/part1/ NEB, IDM, elbow plot, and IRC calculations].		*Tutorial for [https://vasp.at/tutorials/latest/transition_states/part1/ NEB, IDM, elbow plot, and IRC calculations].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part3/ dynamic methods].

	== References ==		== References ==

	[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]		[[Category:VASP\|Transition States]][[Category:Ionic minimization]][[Category:Advanced molecular-dynamics sampling]]

Csheldon at 11:43, 2 June 2025

2025-06-02T11:43:22Z

← Older revision		Revision as of 11:43, 2 June 2025
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	<div style="clear:both;"></div>		<div style="clear:both;"></div>

	= Static methods =		== Static methods ==
	There are three static methods implemented in VASP for finding transition states (TS) using the static, or harmonic, approach: the improved dimer method (IDM), nudged elastic band (NEB), and following the intrinsic reaction coordinate (IRC). IDM takes a guess structure for the TS and then relaxes it along a trial unstable vibrational mode to a first-order saddle point, i.e. the TS. NEB takes the reactant and product structures and interpolates structures between the two to model the reaction pathway. IRC starts at the TS and follows the TS' unstable vibrational mode to reactant and product.		There are three static methods implemented in VASP for finding transition states (TS) using the static, or harmonic, approach: the improved dimer method (IDM), nudged elastic band (NEB), and following the intrinsic reaction coordinate (IRC). IDM takes a guess structure for the TS and then relaxes it along a trial unstable vibrational mode to a first-order saddle point, i.e. the TS. NEB takes the reactant and product structures and interpolates structures between the two to model the reaction pathway. IRC starts at the TS and follows the TS' unstable vibrational mode to reactant and product.

	== Improved dimer method ==		=== Improved dimer method ===
	[[File:idm_single_image.png\|250px\|thumb\|right\|A dimer consisting of two points on the potential energy surface (PES) is rotated to find the lowest curvature. The structure is updated and then a new dimer is defined. The IDM converges towards the desired saddle point, i.e. the TS.]]		[[File:idm_single_image.png\|250px\|thumb\|right\|A dimer consisting of two points on the potential energy surface (PES) is rotated to find the lowest curvature. The structure is updated and then a new dimer is defined. The IDM converges towards the desired saddle point, i.e. the TS.]]
	The dimer method{{Cite\|henkelman:jpc:1999}} is a technique for determining activated transitions without knowledge of the final state. Beginning with a trial transition state (TS) structure, a relaxed TS is obtained. In VASP, the improved dimer method (IDM) by Heyden et al. is implemented. The modification reduces the number of gradient calculations per cycle, improving algorithm performance. A detailed presentation of the method can be found in their paper{{Cite\|heyden:jpc:2005}}. The main tag is {{TAG\|IBRION}}=44.		The dimer method{{Cite\|henkelman:jpc:1999}} is a technique for determining activated transitions without knowledge of the final state. Beginning with a trial transition state (TS) structure, a relaxed TS is obtained. In VASP, the improved dimer method (IDM) by Heyden et al. is implemented. The modification reduces the number of gradient calculations per cycle, improving algorithm performance. A detailed presentation of the method can be found in their paper{{Cite\|heyden:jpc:2005}}. The main tag is {{TAG\|IBRION}}=44.
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	<div style="clear:both;"></div>		<div style="clear:both;"></div>

	== Nudged elastic bands ==		=== Nudged elastic bands ===
	[[File:NEB.png\|300px\|thumb\|right\|The potential energy surface (PES) is described by a series of images (blue) connected by springs (green arrows). The initial (reactant) and final (product) states are shown in black and remain fixed. The TS is the maximum of the PES (red).]]		[[File:NEB.png\|300px\|thumb\|right\|The potential energy surface (PES) is described by a series of images (blue) connected by springs (green arrows). The initial (reactant) and final (product) states are shown in black and remain fixed. The TS is the maximum of the PES (red).]]
	The nudged elastic band (NEB) method{{cite\|mills:surf-sci:1995}}{{cite\|jonsson:book:1998}} involves the creation of an initial path connecting the system's initial and final states, utilizing a set of intermediate configurations ({{TAG\|IMAGES}}). Hence, as a prerequisite, the initial and final state (e.g., reactant and product) must be known. The ''images'' are interconnected by springs ({{TAG\|SPRING}}), forming a flexible ''band''. Through iterative adjustments (''nudging''), the positions of the images along the band are modified, minimizing energy until a minimum energy pathway, referred to as the ''nudged elastic band'', is attained.		The nudged elastic band (NEB) method{{cite\|mills:surf-sci:1995}}{{cite\|jonsson:book:1998}} involves the creation of an initial path connecting the system's initial and final states, utilizing a set of intermediate configurations ({{TAG\|IMAGES}}). Hence, as a prerequisite, the initial and final state (e.g., reactant and product) must be known. The ''images'' are interconnected by springs ({{TAG\|SPRING}}), forming a flexible ''band''. Through iterative adjustments (''nudging''), the positions of the images along the band are modified, minimizing energy until a minimum energy pathway, referred to as the ''nudged elastic band'', is attained.
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	<div style="clear:both;"></div>		<div style="clear:both;"></div>

	== Intrinsic reaction coordinate ==		=== Intrinsic reaction coordinate ===
	[[File:IRC.png\|500px\|thumb\|right\|The potential energy surface (PES) is shown as a contour plot. The IRC begins at TS and follows the associated imaginary frequency <math>u_{\xi}</math> forward to the product P (red) or backward to the reactant R (blue). The energy <math>U(\chi)</math> is plotted against the complex coordinate <math>\chi</math> to illustrate the energy change as the PES is explored.]]		[[File:IRC.png\|500px\|thumb\|right\|The potential energy surface (PES) is shown as a contour plot. The IRC begins at TS and follows the associated imaginary frequency <math>u_{\xi}</math> forward to the product P (red) or backward to the reactant R (blue). The energy <math>U(\chi)</math> is plotted against the complex coordinate <math>\chi</math> to illustrate the energy change as the PES is explored.]]
	Following the intrinsic reaction coordinate (IRC) implies following the steepest descent path from the transition state to reactants and products. The IRC method employs a classical trajectory integration method with fixed velocity, i.e., the damped-velocity Verlet algorithm, incorporating an adaptive time step such that the dynamic reaction pathway resembles the IRC. Hence, as a prerequisite, the transition state must be known. The main tag is {{TAG\|IBRION}}=40.		Following the intrinsic reaction coordinate (IRC) implies following the steepest descent path from the transition state to reactants and products. The IRC method employs a classical trajectory integration method with fixed velocity, i.e., the damped-velocity Verlet algorithm, incorporating an adaptive time step such that the dynamic reaction pathway resembles the IRC. Hence, as a prerequisite, the transition state must be known. The main tag is {{TAG\|IBRION}}=40.
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	<div style="clear:both;"></div>		<div style="clear:both;"></div>

	= Dynamic methods =		== Dynamic methods ==
	An alternative to the static approach for modeling the TS, is to use a dynamic (or anharmonic) approach, that is to use molecular dynamics (MD). The static approach models a single structure for the reactant R, TS, and product P. An MD simulation treats each of these states as an ensemble, a combination of many possible structures.		An alternative to the static approach for modeling the TS, is to use a dynamic (or anharmonic) approach, that is to use molecular dynamics (MD). The static approach models a single structure for the reactant R, TS, and product P. An MD simulation treats each of these states as an ensemble, a combination of many possible structures.

	It is difficult using MD to find uncommon states or rare events, such as the TS. An MD simulation is for a short period of time, typically only femto or picoseconds, while seconds would be required to encounter a TS. However, using constrained MD, e.g. a blue moon simulation{{Cite\|gesvandtnerova:rucco:bucko:2021}}, or metadynamics{{Cite\|klein:2006}}{{Cite\|tiwary:parrinello:2006}}, finding even rare events like the TS becomes feasible. More detail for each of these methods, as well as other advanced MD approaches can be found on the relevant [[:Category:Advanced molecular-dynamics sampling\|advanced MD]] page.		It is difficult using MD to find uncommon states or rare events, such as the TS. An MD simulation is for a short period of time, typically only femto or picoseconds, while seconds would be required to encounter a TS. However, using constrained MD, e.g. a blue moon simulation{{Cite\|gesvandtnerova:rucco:bucko:2021}}, or metadynamics{{Cite\|klein:2006}}{{Cite\|tiwary:parrinello:2006}}, finding even rare events like the TS becomes feasible. More detail for each of these methods, as well as other advanced MD approaches can be found on the relevant [[:Category:Advanced molecular-dynamics sampling\|advanced MD]] page.

	== Tutorials ==		== Additional resources ==
			=== Books and lectures ===
			* Tomáš Bučko has written a book, [https://stella.uniba.sk/texty/PRIF_TB_investigating_chemical_reactions_vasp.pdf Investigating chemical reactions with VASP - A practical guide], to guide in modeling chemical reactions in VASP with accompanying [https://doi.org/10.5281/zenodo.14531578 python scripts]. There are also lectures available on our YouTube channel for modeling chemical reactions (and transition states) using [https://youtu.be/mLK7CtDmw0A static approaches], [https://youtu.be/Rk0S-yvxFUo dynamic approaches], and [https://youtu.be/bzzHpTBwxbA) machine-learned force fields].

			=== Tutorials ===
	*Tutorial for [https://vasp.at/tutorials/latest/transition_states/part1/ NEB, IDM, elbow plot, and IRC calculations].		*Tutorial for [https://vasp.at/tutorials/latest/transition_states/part1/ NEB, IDM, elbow plot, and IRC calculations].
	*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].		*Tutorial for modeling reaction pathways and calculating free energies of reaction using [https://vasp.at/tutorials/latest/transition_states/part2/ static methods].