Nuclephile Substitution CH3Cl - mMD3

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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).

PENALTYPOT

   5.00000   1.00000   9.00000   0.50000
   5.00000   2.00000   9.00000   0.50000
   5.00000   3.00000   9.00000   0.50000
   5.00000   4.00000   9.00000   0.50000
   5.00000   5.00000   9.00000   0.50000
   1.00000   5.00000   9.00000   0.50000
   2.00000   5.00000   9.00000   0.50000
   3.00000   5.00000   9.00000   0.50000
   4.00000   5.00000   9.00000   0.50000

Calculation

Running the calculation

The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.

The bias potential is specified in the PENALTYPOT file.

For practical reasons, we split our (presumably long) meta dynamics calculation into shorter runs of length of 1000 fs (NSW=1000; POTIM=1). At the end of each run the HILLSPOT file (containing bias potential generated in previous run) must be copied to the PENALTYPOT file (the input file with bias potential) - this is done automatically in the script run which looks as follows:

#!/bin/bash

runvasp="mpirun -np x executable_path"

# ensure that this sequence of MD runs is reproducible
cp POSCAR.init POSCAR
cp INCAR.init INCAR
rseed="RANDOM_SEED =         311137787                0                0"
echo $rseed >> INCAR


i=1
while [ $i -le 100 ] 
do

  # start vasp
  $runvasp

  # ensure that this sequence of MD runs is reproducible
  rseed=$(grep RANDOM_SEED REPORT |tail -1)
  cp INCAR.init INCAR
  echo $rseed >> INCAR

  # use bias potential generated in previous mMD run
  cp HILLSPOT PENALTYPOT

  # use the last configuration generated in the previous
  # run as initial configuration for the next run
  cp CONTCAR POSCAR

  # backup some important files
  cp REPORT REPORT.$i
  cp vasprun.xml vasprun.xml.$i

  let i=i+1
done

The user has to adjust the runvasp variable, which holds the command for the executable command.
Please run this script by typing:

bash ./run

Time evolution of distance

During the simulation, the time evolution of collective variable can be monitored using the script timeEv.sh:

#!/bin/bash

rm timeEvol1.dat timeEvol2.dat

i=1
while [ $i -le 1000 ]
do
  if test -f REPORT.$i
  then
    grep fic REPORT.$i |awk '{if (NR%2==1) {print $2} }' >>timeEvol1.dat
    grep fic REPORT.$i |awk '{if (NR%2==0) {print $2} }' >>timeEvol2.dat
  fi
  let i=i+1
done

To execute this script type:

bash ./timeEv.sh

This script creates two files timeEvol1.dat and timeEvol2.dat, which hold the time evolution of the C-Cl distances for both Cl atoms. To visualize that file execute the following command:

gnuplot -e "set terminal jpeg; set xlabel 'timestep'; set ylabel 'Collective variable (Ang)'; set style data lines; plot 'timeEvol1.dat', 'timeEvol2.dat'" > timeEvol.jpg

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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