Nuclephile Substitution CH3Cl - mMD2: Difference between revisions
(Created page with "{{Template:Molecular dynamics - Tutorial}} == Task == In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl via meta...") |
No edit summary |
||
| Line 4: | Line 4: | ||
In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl via meta dynamics is correctly simulated by using extra "repulsive potential walls." | In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl via meta dynamics is correctly simulated by using extra "repulsive potential walls." | ||
== Input == | |||
=== {{TAG|POSCAR}} === | |||
1.00000000000000 | |||
12.0000000000000000 0.0000000000000000 0.0000000000000000 | |||
0.0000000000000000 12.0000000000000000 0.0000000000000000 | |||
0.0000000000000000 0.0000000000000000 12.0000000000000000 | |||
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 | |||
=== {{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}} === | |||
{{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}}=0.0516 | |||
############################# MD setting ##################################### | |||
{{TAGBL|IBRION}}=0 # MD simulation | |||
{{TAGBL|NSW}}=1000 # number of steps | |||
{{TAGBL|POTIM}}=1 # integration step | |||
{{TAGBL|TEBEG}}=600 # 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 | |||
############################################################################## | |||
== Download == | == Download == | ||
Revision as of 15:33, 19 September 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 the nucleophile substitution of a Cl- by another Cl- in CH3Cl via meta dynamics is correctly simulated by using extra "repulsive potential walls."
Input
POSCAR
1.00000000000000
12.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 12.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 12.0000000000000000
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
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
PREC=Low EDIFF=1e-6 LWAVE=.FALSE. LCHARG=.FALSE. NELECT=22 NELMIN=4 LREAL=.FALSE. ALGO=VeryFast ISMEAR=-1 SIGMA=0.0516 ############################# MD setting ##################################### IBRION=0 # MD simulation NSW=1000 # number of steps POTIM=1 # integration step TEBEG=600 # 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 ##############################################################################
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