Nuclephile Substitution CH3Cl - mMD1

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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 HILLS_H and HILLS_W.
• Metadynamics molecular dynamics is formally exact in the limit of infinitesimally small hills (HILLS_H) 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.

ICONST

For this example an ICONST file is used which looks like:

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

• This file is the same as in the previous example Nucleophile Substitution CH3Cl - Standard MD with the exception that the 5 at the fourth entry in the third row specifies that a bias potential is applied to the special coordinate.

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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