Nuclephile Substitution CH3Cl - mMD1 - Revision history

Karsai: /* Download */

2019-11-14T09:45:02Z

Download

← Older revision		Revision as of 09:45, 14 November 2019
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	== Download ==		== Download ==

	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]		[[Media:CH3Cl_mMD1.tgz\| CH3Cl_mMD1.tgz]]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

Karsai: /* Calculation */

2019-09-27T09:52:35Z

Calculation

← Older revision		Revision as of 09:52, 27 September 2019
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	== Calculation ==		== Calculation ==
			As in the previous example ({{TAG\|Nucleophile Substitution CH3Cl - Standard MD}}) the reaction coordinate, the difference between two C-Cl distances, is monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.


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	===Expectation===		===Expectation===
	The meta dynamics simulation pushes the system against the reaction barrier. The amplitude of oscillation of the collective variable increases (as a larger and larger region of configuration space is visited) and at some point the collective variable switches from a positive value (corresponding to the reactant) to a negative value (corresponding to the product).		The meta dynamics simulation pushes the system against the reaction barrier. The amplitude of oscillation of the collective variable increases (as a larger and larger region of configuration space is visited) and at some point the collective variable switches from a positive value (corresponding to the reactant) to a negative value (corresponding to the product).


	===Reality===		===Reality===

Karsai: /* {{TAG|INCAR}} */

2019-09-27T09:50:13Z

← Older revision		Revision as of 09:50, 27 September 2019
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	*Metadynamics molecular dynamics is formally exact in the limit of infinitesimally small hills ({{TAG\|HILLS_H}}) and infinite update time ({{TAG\|HILLS_BIN}}) for the time-dependent bias potential, hence the parameter {{TAG\|\|HILLS_H}} should be as small as possible while {{TAG\|HILLS_BIN}} should be as large as possible.		*Metadynamics molecular dynamics is formally exact in the limit of infinitesimally small hills ({{TAG\|HILLS_H}}) and infinite update time ({{TAG\|HILLS_BIN}}) for the time-dependent bias potential, hence the parameter {{TAG\|\|HILLS_H}} should be as small as possible while {{TAG\|HILLS_BIN}} should be as large as possible.
	*A random seed for reproducibility is used in this calculations which is added later by the ''run'' script.		*A random seed for reproducibility is used in this calculations which is added later by the ''run'' script.
			*Meta dynamics is formally exact in the limit of infinitesimally small hills and infinite update times for the time-dependent bias potential. Hence the parameter {{TAG\|HILLS_H}} should be as small as possible while {{TAG\|HILLS_BIN}} should be as large as possible.

	=== {{TAG\|ICONST}} ===		=== {{TAG\|ICONST}} ===

Karsai: /* Calculation */

2019-09-27T09:48:22Z

Calculation

← Older revision		Revision as of 09:48, 27 September 2019
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	== Calculation ==		== Calculation ==
	For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential). Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.



			=== Running the calculation ===
	The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.		The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.
			For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential). Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.

	~~=== Running the calculation ===~~
	The calculation is executed using the "run" script:		The calculation is executed using the "run" script:
	#!/bin/bash		#!/bin/bash

Karsai: /* Running the calculation */

2019-09-27T09:47:25Z

Running the calculation

← Older revision		Revision as of 09:47, 27 September 2019
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	let i=i+1		let i=i+1
	done		done
	*~~Importantly the~~ user has to adjust the ''runvasp'' variable, which holds the command for the executable command.		*The user has to adjust the ''runvasp'' variable, which holds the command for the executable command.
	*Please run this script by typing:		*Please run this script by typing:
	bash ./run		bash ./run


	===Expectation===		===Expectation===

Karsai: /* Calculation */

2019-09-27T09:46:32Z

Calculation

← Older revision		Revision as of 09:46, 27 September 2019
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	For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential). Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.		For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential). Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.

			The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.

			=== Running the calculation ===
	The calculation is executed using the "run" script:		The calculation is executed using the "run" script:
	#!/bin/bash		#!/bin/bash

Karsai: /* Calculation */

2019-09-27T09:44:55Z

Calculation

← Older revision		Revision as of 09:44, 27 September 2019
Line 70:		Line 70:

	== Calculation ==		== Calculation ==
	For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential).		For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential). Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.



	The calculation is executed using the "run" script:		The calculation is executed using the "run" script:
Line 109:		Line 111:
	let i=i+1		let i=i+1
	done		done
	Please run this script by typing:		*Importantly the user has to adjust the ''runvasp'' variable, which holds the command for the executable command.
			*Please run this script by typing:
	bash ./run		bash ./run
	*Importantly the user has to adjust the ''runvasp'' variable, which holds the command for the executable command.
	*The calculation is run for 50 ps. For convenience the calculation is split into 50 calculations each of length 1 ps.
	*Meta dynamics is a fully stochastic simulation, the results can depend on the random numbers used in the calculations. To ensure best reproducibility the calculation is started from the same random seed (''rseed="RANDOM_SEED = 311137787 0 0"''). After each step the last random seed is copied to the {{TAG\|INCAR}} file for the new step. This way reproducability is ensured between each step.

Karsai: /* Calculation */

2019-09-27T09:43:41Z

Calculation

← Older revision		Revision as of 09:43, 27 September 2019
Line 70:		Line 70:

	== Calculation ==		== Calculation ==
			For practical reasons, we split our (pressumably long) meta dynamics calculation into shorter runs of length of 1000 fs for each ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run, the {{TAG\|HILLSPOT}} file (containing the bias potential generated in the previous run) must be copied to the {{TAG\|PENALTYPOT}} file (the input file with bias potential).

	The calculation is executed using the "run" script:		The calculation is executed using the "run" script:
	#!/bin/bash		#!/bin/bash

Karsai: Karsai moved page Nuclephile Substitution CH3Cl - mMD to Nuclephile Substitution CH3Cl - mMD1

2019-09-26T11:42:03Z

Karsai moved page Nuclephile Substitution CH3Cl - mMD to Nuclephile Substitution CH3Cl - mMD1

← Older revision	Revision as of 11:42, 26 September 2019
(No difference)

Karsai at 09:17, 26 September 2019

2019-09-26T09:17:27Z

← Older revision		Revision as of 09:17, 26 September 2019
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	== Download ==		== Download ==

			[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]