Nucleophile Substitution CH3Cl - Standard MD: Difference between revisions
| Line 51: | Line 51: | ||
############################################################################## | ############################################################################## | ||
* | *Molecular dynamics are switched on by the tag {{TAGBL|IBRION}}=0. | ||
*The metadynamics tag {{TAGBL|MDALGO}}=11 is only used to monitor the two C-Cl distances defined in the {{TAG|ICONST}} file. | *The metadynamics tag {{TAGBL|MDALGO}}=11 is only used to monitor the two C-Cl distances defined in the {{TAG|ICONST}} file. | ||
*Simulations are carried out in the {{TAG|NVT ensemble}} at approximately room temperature ({{TAGBL|TEBEG}}=300) and the Anderson thermostat is used for the temperature control. | *Simulations are carried out in the {{TAG|NVT ensemble}} at approximately room temperature ({{TAGBL|TEBEG}}=300) and the Anderson thermostat is used for the temperature control. The strength of the coupling is controlled by the collision probability {TAGBL|ANDERSEN_PROB}}=0.10. | ||
*The accuracy of this calculation is kept low ({{TAGBL|PREC}}=Low and {{TAGBL|ALGO}}=VeryFast), which is completely sufficient for this tutorial. For more quantitative results this tags should be changed (of course at the cost of higher computational demand). | |||
=== {{TAG|ICONST}} === | === {{TAG|ICONST}} === | ||
Revision as of 15:36, 7 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
The main task of this example is to model a nucleophile substitution of CH3Cl by Cl-.
Input
POSCAR
CH3Cl
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
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
PREC=Low EDIFF=1e-6 LWAVE=.FALSE. LCHARG=.FALSE. NELECT=22 NELMIN=4 LREAL=.FALSE. ALGO=VeryFast ISMEAR=-1 SIGMA=0.0258 ############################# 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 ##############################################################################
- Molecular dynamics are switched on by the tag IBRION=0.
- The metadynamics tag MDALGO=11 is only used to monitor the two C-Cl distances defined in the ICONST file.
- Simulations are carried out in the NVT ensemble at approximately room temperature (TEBEG=300) and the Anderson thermostat is used for the temperature control. The strength of the coupling is controlled by the collision probability {TAGBL|ANDERSEN_PROB}}=0.10.
- The accuracy of this calculation is kept low (PREC=Low and ALGO=VeryFast), which is completely sufficient for this tutorial. For more quantitative results this tags should be changed (of course at the cost of higher computational demand).
ICONST
For this example an ICONST file is used
R 1 5 0 R 1 6 0 S 1 -1 7