Nuclephile Substitution CH3Cl - mMD3: Difference between revisions

Revision as of 11:49, 27 September 2019

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 the nucleophile substitution of a Cl^- by another Cl^- in CH₃Cl via meta dynamics is simulated using two collective variables simultaneously.

Input

POSCAR

   1.00000000000000
     9.0000000000000000    0.0000000000000000    0.0000000000000000
     0.0000000000000000    9.0000000000000000    0.0000000000000000
     0.0000000000000000    0.0000000000000000    9.0000000000000000
   C    H    Cl
   1   3   2
Direct
  0.1570348572197245  0.2904054711139102  0.1422643997559632
  0.1466469234176954  0.4066467848992589  0.1077433527138946
  0.0469134772399311  0.2399491465236156  0.1544210764126938
  0.2197893311177821  0.2820094213788985  0.2462070949679763
  0.9809163623144840  0.4723904404063168  0.3674924467383788
  0.2601754409903839  0.1874592103557934  0.9964911656110944

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=1000                                           # 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
##############################################################################

ICONST

R 1 5 5
R 1 6 5

In contrast to the previous examples two collective variables are used simultaneously (and no combination of them).

Calculation

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

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 {{Template:Molecular dynamics - Tutorial}}
+== Task ==
+In this example the nucleophile substitution of a Cl<sup>-</sup> by another Cl<sup>-</sup> in CH<sub>3</sub>Cl via meta dynamics is simulated using two collective variables simultaneously.
+== Input ==
+=== {{TAG|POSCAR}} ===
+.00000000000000
+.0000000000000000    0.0000000000000000    0.0000000000000000
+.0000000000000000    9.0000000000000000    0.0000000000000000
+.0000000000000000    0.0000000000000000    9.0000000000000000
+    C    H    Cl
+   3   2
+ Direct
+.1570348572197245  0.2904054711139102  0.1422643997559632
+.1466469234176954  0.4066467848992589  0.1077433527138946
+.0469134772399311  0.2399491465236156  0.1544210764126938
+.2197893311177821  0.2820094213788985  0.2462070949679763
+.9809163623144840  0.4723904404063168  0.3674924467383788
+.2601754409903839  0.1874592103557934  0.9964911656110944
+=== {{TAG|KPOINTS}} ===
+ Automatic
+ Gamma
+  1  1
+. 0. 0.
+*For isolated atoms and molecules interactions between periodic images are negligible (in sufficiently large cells) hence no Brillouin zone sampling is necessary.
+=== {{TAG|INCAR}} ===
+ {{TAGBL|PREC}}=Low
+ {{TAGBL|EDIFF}}=1e-6
+ {{TAGBL|LWAVE}}=.FALSE.
+ {{TAGBL|LCHARG}}=.FALSE.
+ {{TAGBL|NELECT}}=22
+ {{TAGBL|NELMIN}}=4
+ {{TAGBL|LREAL}}=.FALSE.
+ {{TAGBL|ALGO}}=VeryFast
+ {{TAGBL|ISMEAR}}=-1
+ {{TAGBL|SIGMA}}=0.0516
+ ############################# MD setting #####################################
+ {{TAGBL|IBRION}}=0                                           # MD simulation
+ {{TAGBL|NSW}}=1000                                           # number of steps
+ {{TAGBL|POTIM}}=1                                            # integration step
+ {{TAGBL|TEBEG}}=600                                          # simulation temperature
+ {{TAGBL|MDALGO}}=11                                          # metaDynamics with Andersen thermostat
+ {{TAGBL|ANDERSEN_PROB}}=0.10                                 # collision probability
+ {{TAGBL|HILLS_BIN}}=50                                       # update the time-dependent bias
+                                                              # potential every 50 steps
+ {{TAGBL|HILLS_H}}=0.005                                      # height of the Gaussian
+ {{TAGBL|HILLS_W}}=0.05                                       # width of the Gaussian
+ ##############################################################################
+=== {{TAG|ICONST}} ===
+ R 1 5 5
+ R 1 6 5
+*In contrast to the previous examples two collective variables are used simultaneously (and no combination of them).
+== Calculation ==
 == Download ==