Nuclephile Substitution CH3Cl - mMD1: Difference between revisions

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=== {{TAG|INCAR}} ===
=== {{TAG|INCAR}} ===
  ############################# MD setting #####################################
  {{TAGBL|PREC}}=Low
  {{TAGBL|IBRION}} = 0                                          # MD simulation
{{TAGBL|EDIFF}}=1e-6
  {{TAGBL|NSW}} = 1000                                           # number of steps
{{TAGBL|LWAVE}}=.FALSE.
  {{TAGBL|POTIM}} = 1                                            # integration step
{{TAGBL|LCHARG}}=.FALSE.
  {{TAGBL|TEBEG}} = 300                                         # simulation temperature
{{TAGBL|NELECT}}=22
  {{TAGBL|MDALGO}} = 11                                          # metaDynamics with Andersen thermostat
{{TAGBL|NELMIN}}=4
  {{TAGBL|ANDERSEN_PROB}} = 0.10                                # collision probability
{{TAGBL|LREAL}}=.FALSE.
  {{TAGBL|HILLS_BIN}} = 50                                      # update the time-dependent bias
{{TAGBL|ALGO}}=VeryFast
                                                                # potential every 50 steps
{{TAGBL|ISMEAR}}=-1
  {{TAGBL|HILLS_H}} = 0.005                                      # height of the Gaussian
{{TAGBL|SIGMA}}=0.0516
  {{TAGBL|HILLS_W}} = 0.05                                      # width of the Gaussian
 
##############################################################################  
############################# MD setting #####################################
  {{TAGBL|IBRION}}=0                                          # MD simulation
{{TAGBL|PREC}} = Low
  {{TAGBL|NSW}}=50000                                           # number of steps
{{TAGBL|EDIFF}} = 1e-6
  {{TAGBL|POTIM}}=1                                            # integration step
{{TAGBL|LWAVE}} = .FALSE.
  {{TAGBL|TEBEG}}=600                                         # simulation temperature
{{TAGBL|LCHARG}} = .FALSE.
  {{TAGBL|MDALGO}}=11                                          # metaDynamics with Andersen thermostat
{{TAGBL|NELECT}} = 22
  {{TAGBL|ANDERSEN_PROB}}=0.10                                # collision probability
{{TAGBL|NELMIN}} = 4
  {{TAGBL|HILLS_BIN}}=50                                      # update the time-dependent bias
{{TAGBL|LREAL}} = .FALSE.
                                                  # potential every 50 steps
{{TAGBL|ALGO}} = VeryFast
  {{TAGBL|HILLS_H}}=0.005                                      # height of the Gaussian
{{TAGBL|ISMEAR}} = -1
  {{TAGBL|HILLS_W}}=0.05                                      # width of the Gaussian
{{TAGBL|SIGMA}} = 0.0258
##############################################################################
 


*The {{TAG|INCAR}} file in this example is the same as in the previous example ({{TAG|Nucleophile Substitution CH3Cl - Standard MD}}) with the exception of the metadynamics tags. For explanation of the tags please have a look at that example.
*The {{TAG|INCAR}} file in this example is the same as in the previous example ({{TAG|Nucleophile Substitution CH3Cl - Standard MD}}) with the exception of the metadynamics tags. For explanation of the tags please have a look at that example.

Revision as of 11:16, 19 September 2019

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
                                                          1. 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. 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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