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
##############################################################################

• 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).
• 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.

ICONST

For this example an ICONST file is used

R 1 5 0
R 1 6 0
S 1 -1 7