Nuclephile Substitution CH3Cl - mMD1: Difference between revisions
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{{Template:Molecular dynamics - Tutorial}} | |||
== Task == | |||
In this example a nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl is attempted via a meta dynamics calculation. | |||
== Input == | == Input == | ||
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*The starting {{TAG|POSCAR}} file for this example can be found under POSCAR.init. It will be needed for the script that runs the job (run.sh). | *The starting {{TAG|POSCAR}} file for this example can be found under POSCAR.init. It will be needed for the script that runs the job (run.sh). | ||
*A sufficiently large cell is chosen to minimize the interactions between neighbouring cells and hence to simulate an isolated molecular reaction. | *A sufficiently large cell is chosen to minimize the interactions between neighbouring cells and hence to simulate an isolated molecular reaction. | ||
=== {{TAG|KPOINTS}} === | |||
Automatic | |||
0 | |||
Gamma | |||
1 1 1 | |||
0. 0. 0. | |||
*For isolated atoms and molecules interactions between periodic images are negligible (in sufficiently large cells) hence no Brillouin zone sampling is necessary. | |||
=== {{TAG|INCAR}} === | |||
############################# MD setting ##################################### | |||
{{TAGBL|IBRION}} = 0 # MD simulation | |||
{{TAGBL|NSW}} = 1000 # number of steps | |||
{{TAGBL|POTIM}} = 1 # integration step | |||
{{TAGBL|TEBEG}} = 300 # simulation temperature | |||
{{TAGBL|MDALGO}} = 11 # metaDynamics with Andersen thermostat | |||
{{TAGBL|ANDERSEN_PROB}} = 0.10 # collision probability | |||
{{TAGBL|HILLS_BIN}} = 50 # update the time-dependent bias | |||
# potential every 50 steps | |||
{{TAGBL|HILLS_H}} = 0.005 # height of the Gaussian | |||
{{TAGBL|HILLS_W}} = 0.05 # width of the Gaussian | |||
############################################################################## | |||
{{TAGBL|PREC}} = Low | |||
{{TAGBL|EDIFF}} = 1e-6 | |||
{{TAGBL|LWAVE}} = .FALSE. | |||
{{TAGBL|LCHARG}} = .FALSE. | |||
{{TAGBL|NELECT}} = 22 | |||
{{TAGBL|NELMIN}} = 4 | |||
{{TAGBL|LREAL}} = .FALSE. | |||
{{TAGBL|ALGO}} = VeryFast | |||
{{TAGBL|ISMEAR}} = -1 | |||
{{TAGBL|SIGMA}} = 0.0258 | |||
== Download == | |||
{{Template:Molecular dynamics - Tutorial}} | |||
[[Category:Examples]] | |||
Revision as of 11:13, 29 June 2019
Overview >Liquid Si - Standard MD > Liquid Si - Freezing > Nucleophile Substitution CH3Cl - Standard MD > Nuclephile Substitution CH3Cl - mMD1 > Nuclephile Substitution CH3Cl - mMD2 > Nuclephile Substitution CH3Cl - mMD3 > Nuclephile Substitution CH3Cl - SG > Nuclephile Substitution CH3Cl - BM > List of tutorials
Task
In this example a nucleophile substitution of a Cl- by another Cl- in CH3Cl is attempted via a meta dynamics calculation.
Input
POSCAR
1.00000000000000
12.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 12.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 12.0000000000000000
C H Cl
1 3 2
cart
5.91331371 7.11364924 5.78037960
5.81982231 8.15982106 5.46969017
4.92222130 6.65954232 5.88978969
6.47810398 7.03808479 6.71586385
4.32824726 8.75151396 7.80743202
6.84157897 6.18713289 4.46842049
- The starting POSCAR file for this example can be found under POSCAR.init. It will be needed for the script that runs the job (run.sh).
- A sufficiently large cell is chosen to minimize the interactions between neighbouring cells and hence to simulate an isolated molecular reaction.
KPOINTS
Automatic 0 Gamma 1 1 1 0. 0. 0.
- For isolated atoms and molecules interactions between periodic images are negligible (in sufficiently large cells) hence no Brillouin zone sampling is necessary.
INCAR
############################# MD setting ##################################### IBRION = 0 # MD simulation NSW = 1000 # number of steps POTIM = 1 # integration step TEBEG = 300 # simulation temperature MDALGO = 11 # metaDynamics with Andersen thermostat ANDERSEN_PROB = 0.10 # collision probability HILLS_BIN = 50 # update the time-dependent bias # potential every 50 steps HILLS_H = 0.005 # height of the Gaussian HILLS_W = 0.05 # width of the Gaussian ############################################################################## PREC = Low EDIFF = 1e-6 LWAVE = .FALSE. LCHARG = .FALSE. NELECT = 22 NELMIN = 4 LREAL = .FALSE. ALGO = VeryFast ISMEAR = -1 SIGMA = 0.0258
Download
Overview >Liquid Si - Standard MD > Liquid Si - Freezing > Nucleophile Substitution CH3Cl - Standard MD > Nuclephile Substitution CH3Cl - mMD1 > Nuclephile Substitution CH3Cl - mMD2 > Nuclephile Substitution CH3Cl - mMD3 > Nuclephile Substitution CH3Cl - SG > Nuclephile Substitution CH3Cl - BM > List of tutorials