Nuclephile Substitution CH3Cl - mMD1: Difference between revisions
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=== {{TAG|INCAR}} === | === {{TAG|INCAR}} === | ||
############################# MD setting ##################################### | {{TAGBL|PREC}}=Low | ||
{{TAGBL|IBRION}} = 0 # MD simulation | {{TAGBL|EDIFF}}=1e-6 | ||
{{TAGBL|NSW}} = | {{TAGBL|LWAVE}}=.FALSE. | ||
{{TAGBL|POTIM}} = 1 # integration step | {{TAGBL|LCHARG}}=.FALSE. | ||
{{TAGBL|TEBEG}} = | {{TAGBL|NELECT}}=22 | ||
{{TAGBL|MDALGO}} = 11 # metaDynamics with Andersen thermostat | {{TAGBL|NELMIN}}=4 | ||
{{TAGBL|ANDERSEN_PROB}} = 0.10 # collision probability | {{TAGBL|LREAL}}=.FALSE. | ||
{{TAGBL|HILLS_BIN}} = 50 # update the time-dependent bias | {{TAGBL|ALGO}}=VeryFast | ||
{{TAGBL|ISMEAR}}=-1 | |||
{{TAGBL|HILLS_H}} = 0.005 # height of the Gaussian | {{TAGBL|SIGMA}}=0.0516 | ||
{{TAGBL|HILLS_W}} = 0.05 # width of the Gaussian | |||
############################# MD setting ##################################### | |||
{{TAGBL|IBRION}}=0 # MD simulation | |||
{{TAGBL|NSW}}=50000 # 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 | |||
############################################################################## | |||
*The {{TAG|INCAR}} file in this example is the same as in the previous example ({{TAG|Nucleophile Substitution CH3Cl - Standard MD}}) with the exception of the metadynamics tags. For explanation of the tags please have a look at that example. | *The {{TAG|INCAR}} file in this example is the same as in the previous example ({{TAG|Nucleophile Substitution CH3Cl - Standard MD}}) with the exception of the metadynamics tags. For explanation of the tags please have a look at that example. | ||
Revision as of 11:16, 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 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
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=50000 # 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
- The INCAR file in this example is the same as in the previous example (Nucleophile Substitution CH3Cl - Standard MD) with the exception of the metadynamics tags. For explanation of the tags please have a look at that example.
- Metadynamics molecular dynamics is formally exact in the limit of infinitesimally small hills ([[]]) and infinite update time (HILLS_BIN) for the time-dependent bias potential, hence the parameter [[]]should be as small as possible while HILLS_BIN should be as large as possible.
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