Nucleophile Substitution CH3Cl - Standard MD

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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