Nuclephile Substitution CH3Cl - mMD2 - Revision history

Karsai: /* Download */

2019-11-14T09:45:23Z

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_mMD2.tgz CH3Cl_mMD2.tgz]		[[Media:CH3Cl_mMD2.tgz\| CH3Cl_mMD2.tgz]]

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

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

Karsai: /* Calculation */

2019-10-03T08:49:59Z

Calculation

← Older revision		Revision as of 08:49, 3 October 2019
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	=== Running the calculation ===		=== 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 (note that the free energy is independent of the masses of atoms).

	The bias potential is specified in the {{TAG\|PENALTYPOT}} file.		The bias potential is specified in the {{TAG\|PENALTYPOT}} file.

Karsai: /* Free-energy profile */

2019-10-01T09:16:16Z

Free-energy profile

← Older revision		Revision as of 09:16, 1 October 2019
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	If everything goes well, you should observe that the amplitude of oscillations of the collective variable increases (as larger and larger region of configuration space is visited by the meta dynamics) and at some poin the collective variable switches from a positive value (corresponding to reactant) to a negative value (correpsonding to product). At the end of your calculation, you should observe depending on how long you ran the calculation (50 or more ps) one or two crossings of the transition state (where the collective variable is equal to zero).		If everything goes well, you should observe that the amplitude of oscillations of the collective variable increases (as larger and larger region of configuration space is visited by the meta dynamics) and at some poin the collective variable switches from a positive value (corresponding to reactant) to a negative value (correpsonding to product). At the end of your calculation, you should observe depending on how long you ran the calculation (50 or more ps) one or two crossings of the transition state (where the collective variable is equal to zero).

	=== ~~Free~~-energy profile ===		=== 1D free-energy profile ===
	The current bias potential generated by meta dynamics is written to the {{TAG\|HILLSPOT}} file. A negative image of this potential serves as an approximation of the free-energy profile and it can be visualized using the script ''calcprofile1D.py'':		The current bias potential generated by meta dynamics is written to the {{TAG\|HILLSPOT}} file. A negative image of this potential serves as an approximation of the free-energy profile and it can be visualized using the script ''calcprofile1D.py'':
	#!/usr/bin/python		#!/usr/bin/python

Karsai: /* Time evolution of distance */

2019-09-30T10:32:16Z

Time evolution of distance

← Older revision		Revision as of 10:32, 30 September 2019
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	=== Time evolution of distance ===		=== Time evolution of distance ===

	During the simulation, time evolution of collective variable can be monitored using the script ''timeEv.sh'':		During the simulation, the time evolution of collective variable can be monitored using the script ''timeEv.sh'':
	#!/bin/bash		#!/bin/bash

Karsai at 11:51, 27 September 2019

2019-09-27T11:51:21Z

← Older revision		Revision as of 11:51, 27 September 2019
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	S 1 -1 5		S 1 -1 5
	*This file is the same as in the previous example ({{TAG\|Nuclephile Substitution CH3Cl - mMD1}}).		*This file is the same as in the previous example ({{TAG\|Nuclephile Substitution CH3Cl - mMD1}}).

			=== {{TAG\|PENALTYPOT}} ===
			-3.00000 1.00000 0.30000
			3.00000 1.00000 0.30000

	== Calculation ==		== Calculation ==

Karsai: /* Free-energy profile */

2019-09-27T11:00:15Z

Free-energy profile

← Older revision		Revision as of 11:00, 27 September 2019
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	''x1_min x1_max N:''		''x1_min x1_max N:''
	-5 5 500		-5 5 500
	~~[http://www.vasp.at/vasp-workshop/exam[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]ples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]~~
	To plot the 1D free energy profile type:		To plot the 1D free energy profile type:
	gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg

Karsai at 10:59, 27 September 2019

2019-09-27T10:59:49Z

← Older revision		Revision as of 10:59, 27 September 2019
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	en_=gauss_pot(x,x0,h[j],w[j])		en_=gauss_pot(x,x0,h[j],w[j])
	en+=en_		en+=en_
	ff.write(`x`+'\t'+`-en`+'\n')		ff.write(`x`+'\t'+`-en`+'\n')[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]
	ff.close()		ff.close()
	This script projects one-dimensional Gaussians defined in the input file (such as {{TAG\|PENALTYPOT}} or {{TAG\|HILLSPOT}}) onto a regular grid of <math>N</math> points defined by a user. The user is asked to provide the following data: (a) name of the input file, (b) the initial (x1_min) and the final (x1_max) grid point position, and the number of grid points (M) for the axis corresponding to the collective variable. The result is written in file with extension ''.xyz''.		This script projects one-dimensional Gaussians defined in the input file (such as {{TAG\|PENALTYPOT}} or {{TAG\|HILLSPOT}}) onto a regular grid of <math>N</math> points defined by a user. The user is asked to provide the following data: (a) name of the input file, (b) the initial (x1_min) and the final (x1_max) grid point position, and the number of grid points (M) for the axis corresponding to the collective variable. The result is written in file with extension ''.xyz''.
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	''x1_min x1_max N:''		''x1_min x1_max N:''
	-5 5 500		-5 5 500
			[http://www.vasp.at/vasp-workshop/exam[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]ples/CH3Cl_mMD1.tgz CH3Cl_mMD1.tgz]
	To plot the 1D free energy profile type:		To plot the 1D free energy profile type:
	gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg
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	== Download ==		== Download ==

			[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD2.tgz CH3Cl_mMD2.tgz]

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

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

Karsai: /* Free-energy profile */

2019-09-27T10:54:49Z

Free-energy profile

← Older revision		Revision as of 10:54, 27 September 2019
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	gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg
	The resulting free energy profile should look like the following:		The resulting free energy profile should look like the following:

	[[File:1D free energy CHCl3 mMD2.jpg\|500px]]		[[File:1D free energy CHCl3 mMD2.jpg\|500px]]

Karsai: /* Free-energy profile */

2019-09-27T10:54:37Z

Free-energy profile

← Older revision		Revision as of 10:54, 27 September 2019
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	To plot the 1D free energy profile type:		To plot the 1D free energy profile type:
	gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg
			The resulting free energy profile should look like the following:
			[[File:1D free energy CHCl3 mMD2.jpg\|500px]]

	== Download ==		== Download ==

Karsai: /* Free-energy profile */

2019-09-27T10:53:14Z

Free-energy profile

← Older revision		Revision as of 10:53, 27 September 2019
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	''x1_min x1_max N:''		''x1_min x1_max N:''
	-5 5 500		-5 5 500

			To plot the 1D free energy profile type:
			gnuplot -e "set terminal jpeg; set xlabel 'r (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'HILLSPOT.xyz'" > 1D_free_energy.jpg

	== Download ==		== Download ==