Nuclephile Substitution CH3Cl - BM - Revision history

Karsai: /* Running the calculation */

2022-07-19T08:46:08Z

Running the calculation

← Older revision		Revision as of 08:46, 19 July 2022
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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 (note that the free energy is independent of the masses of atoms).		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 simulation for each of the points along the reaction coordinate is performed in a separate directory called ''1, 2, ..., 7''. These are created automatically by the run script. For practical reasons, we split our (presumably long) blue moon calculation into shorter runs of length of 1000 fs ({{TAG\|NSW}}=1000; {{TAG\|POTIM}}=1). This is done automatically in the script ''run'' which looks as follows:		The simulation for each of the points along the reaction coordinate is performed in a separate directory called ''1, 2, ..., 7''. These are created automatically by the run script. For practical reasons, we split our (presumably long) blue-moon calculation into shorter runs of length of 1000 fs ({{TAG\|NSW}}=1000; {{TAG\|POTIM}}=1). This is done automatically in the script ''run'' which looks as follows:
	#!/bin/bash		#!/bin/bash

Karsai: /* Calculation */

2022-07-19T08:45:46Z

Calculation

← Older revision		Revision as of 08:45, 19 July 2022
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	== Calculation ==		== Calculation ==

	In the blue moon ~~method~~, the free energy difference is computed by integration of the free energy gradients computed for several points differing in the value of the collective variable distributed between known inital and final states. The gradients for each point are computed within a constrained molecular dynamics simulation (note the value of ''STATUS''=0 for the collective variable defined in the {{TAG\|ICONST}} file).		In the [[Blue-moon ensemble\|blue-moon sampling]], the free energy difference is computed by integration of the free energy gradients computed for several points differing in the value of the collective variable distributed between known inital and final states. The gradients for each point are computed within a constrained molecular dynamics simulation (note the value of ''STATUS''=0 for the collective variable defined in the {{TAG\|ICONST}} file).

	=== Running the calculation ===		=== Running the calculation ===

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

2022-07-19T08:45:00Z

← Older revision		Revision as of 08:45, 19 July 2022
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	=== {{TAG\|POSCAR}} ===		=== {{TAG\|POSCAR}} ===
	In the blue moon sampling method several {{TAG\|POSCAR}} files are used for different values of the collective variable.		In the [[Blue-moon ensemble\|blue-moon sampling]] method several {{TAG\|POSCAR}} files are used for different values of the collective variable.

	<div class="toccolours mw-customtoggle-script">'''Click to show/POSCARs'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/POSCARs'''</div>

Karsai: /* Task */

2022-07-19T08:44:32Z

Task

← Older revision		Revision as of 08:44, 19 July 2022
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	== Task ==		== Task ==
	In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl is simulated using ~~bluemoon~~ sampling.		In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl is simulated using [[Blue-moon ensemble\|blue-moon sampling]].

	== Input ==		== Input ==

Karsai: /* Free-energy profile */

2022-04-15T15:11:49Z

Free-energy profile

@@ Line 274: / Line 274: @@
 The free energy vs. collective variable is obtained by forward integration using the script ''integrateForward.py'':
 <div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
-<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>
+<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
 To execute that script type and write to the file ''free_energy.dat'':

Karsai: /* Free-energy profile */

2022-04-15T15:10:11Z

Free-energy profile

@@ Line 220: / Line 220: @@
 The free energy gradient is obtained as a ratio of two averages (see {{TAG|Constrained molecular dynamics}}). This is done by the script ''fgradBM.sh'', which writes the free energy gradient vs. the collective variable to the file ''grad.dat'':
 <div class="toccolours mw-customtoggle-script">'''Click to show/fgradBM.sh'''</div>
-<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:fgradBM_CH3Cl_BM}}</div>
+<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
 To execute that script type:

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

2022-04-15T15:08:54Z

@@ Line 10: / Line 10: @@
 <div class="toccolours mw-customtoggle-script">'''Click to show/POSCARs'''</div>
-<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:POSCAR_CH3Cl_BM}}</div>
+<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
 === {{TAG|KPOINTS}} ===

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

2020-01-21T13:02:02Z

← Older revision		Revision as of 13:02, 21 January 2020
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	{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability		{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability
	{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to		{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to
	# compute free-energy gradient		# compute free-energy gradient
	##############################################################################		##############################################################################

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

2020-01-21T13:01:53Z

← Older revision		Revision as of 13:01, 21 January 2020
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	{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability		{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability
	{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to		{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to
	# compute free-energy gradient		# compute free-energy gradient
	##############################################################################		##############################################################################

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

2020-01-21T13:01:41Z

← Older revision		Revision as of 13:01, 21 January 2020
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	=== {{TAG\|INCAR}} ===		=== {{TAG\|INCAR}} ===
	~~<pre>~~
	{{TAGBL\|PREC}}=Low		{{TAGBL\|PREC}}=Low
	{{TAGBL\|EDIFF}}=1e-6		{{TAGBL\|EDIFF}}=1e-6
	{{TAGBL\|LWAVE}}=.FALSE.		{{TAGBL\|LWAVE}}=.FALSE.
	{{TAGBL\|LCHARG}}=.FALSE.		{{TAGBL\|LCHARG}}=.FALSE.
	{{TAGBL\|NELECT}}=22		{{TAGBL\|NELECT}}=22
	{{TAGBL\|NELMIN}}=4		{{TAGBL\|NELMIN}}=4
	{{TAGBL\|LREAL}}=.FALSE.		{{TAGBL\|LREAL}}=.FALSE.
	{{TAGBL\|ALGO}}=VeryFast		{{TAGBL\|ALGO}}=VeryFast
	{{TAGBL\|ISMEAR}}=-1		{{TAGBL\|ISMEAR}}=-1
	{{TAGBL\|SIGMA}}=0.0516		{{TAGBL\|SIGMA}}=0.0516

	############################# MD setting ##################################		############################# MD setting ##################################
	{{TAGBL\|IBRION}}=0 # MD simulation		{{TAGBL\|IBRION}}=0 # MD simulation
	{{TAGBL\|NSW}}=1000 # number of steps		{{TAGBL\|NSW}}=1000 # number of steps
	{{TAGBL\|POTIM}}=1 # integration step		{{TAGBL\|POTIM}}=1 # integration step
	{{TAGBL\|TEBEG}}=600 # simulation temperature		{{TAGBL\|TEBEG}}=600 # simulation temperature
	{{TAGBL\|MDALGO}}=11 # Andersen thermostat		{{TAGBL\|MDALGO}}=11 # Andersen thermostat
	{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability		{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability
	{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to		{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to
	# compute free-energy gradient		# compute free-energy gradient
	##############################################################################		##############################################################################
	~~</pre>~~

	*The setting {{TAG\|LBLUEOUT}}=''.TRUE.'' tells VASP to write out the information needed for the computation of free energies.		*The setting {{TAG\|LBLUEOUT}}=''.TRUE.'' tells VASP to write out the information needed for the computation of free energies.

← Older revision		Revision as of 13:01, 21 January 2020
Line 24:		Line 24:

	=== {{TAG\|INCAR}} ===		=== {{TAG\|INCAR}} ===
	~~<pre>~~
	{{TAGBL\|PREC}}=Low		{{TAGBL\|PREC}}=Low
	{{TAGBL\|EDIFF}}=1e-6		{{TAGBL\|EDIFF}}=1e-6
	{{TAGBL\|LWAVE}}=.FALSE.		{{TAGBL\|LWAVE}}=.FALSE.
	{{TAGBL\|LCHARG}}=.FALSE.		{{TAGBL\|LCHARG}}=.FALSE.
	{{TAGBL\|NELECT}}=22		{{TAGBL\|NELECT}}=22
	{{TAGBL\|NELMIN}}=4		{{TAGBL\|NELMIN}}=4
	{{TAGBL\|LREAL}}=.FALSE.		{{TAGBL\|LREAL}}=.FALSE.
	{{TAGBL\|ALGO}}=VeryFast		{{TAGBL\|ALGO}}=VeryFast
	{{TAGBL\|ISMEAR}}=-1		{{TAGBL\|ISMEAR}}=-1
	{{TAGBL\|SIGMA}}=0.0516		{{TAGBL\|SIGMA}}=0.0516

	############################# MD setting ##################################		############################# MD setting ##################################
	{{TAGBL\|IBRION}}=0 # MD simulation		{{TAGBL\|IBRION}}=0 # MD simulation
	{{TAGBL\|NSW}}=1000 # number of steps		{{TAGBL\|NSW}}=1000 # number of steps
	{{TAGBL\|POTIM}}=1 # integration step		{{TAGBL\|POTIM}}=1 # integration step
	{{TAGBL\|TEBEG}}=600 # simulation temperature		{{TAGBL\|TEBEG}}=600 # simulation temperature
	{{TAGBL\|MDALGO}}=11 # Andersen thermostat		{{TAGBL\|MDALGO}}=11 # Andersen thermostat
	{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability		{{TAGBL\|ANDERSEN_PROB}}=0.10 # collision probability
	{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to		{{TAGBL\|LBLUEOUT}}=.TRUE. # write down output needed to
	# compute free-energy gradient		# compute free-energy gradient
	##############################################################################		##############################################################################
	~~</pre>~~

	*The setting {{TAG\|LBLUEOUT}}=''.TRUE.'' tells VASP to write out the information needed for the computation of free energies.		*The setting {{TAG\|LBLUEOUT}}=''.TRUE.'' tells VASP to write out the information needed for the computation of free energies.