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

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

PREC = Low
EDIFF = 1e-6
LWAVE = .FALSE.
LCHARG = .FALSE.
NELECT = 22
NELMIN = 4
LREAL = .FALSE.
ALGO = VeryFast
ISMEAR = -1
SIGMA = 0.0258

• 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.

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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