Nuclephile Substitution CH3Cl - mMD1

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 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

• First line: This line selects the interatomic distance (R) between the first (C) and the fifth atom (Cl) in the POSCAR file. The 0 at the fourth entry would usually specify that the distances are constrained but if the coordinates are used later for special coordinates the constraining is not applied (for further information see ICONST).
• Second line: Same as the first line but interatomic distance between the first (C) and the sixth atom (Cl) in the POSCAR file is selected.
• Third line: This line selects a linear combination (option S) of the first two coordinates where the second and fourth column specify the coefficients of the coordinates. The setting of 1 and -1 corresponds to the difference between both. The 5 at the fourth entry specifies that a bias potential is applied to the special coordinate.

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