Nuclephile Substitution CH3Cl - mMD2: Difference between revisions
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== Calculation == | == Calculation == | ||
In principle, meta dynamics always seeks for the path of least resistance. In the case of our model system this corresponds to the dissociation of the vdW complex (which is linked with a lower barrier than the SN2 reaction). In order to avoid this undesired process, an extra bias potential ("repulsive walls") is used whose role is to restrict our sampling to a relevant region (approx. <math>-3 \AA < </math> collective variable <math>< 3 A</math>). In fact, the positions of walls can be chosen arbitrarily - we only require that the region between the walls contains all the information we are interested in (in this case we want to see free-energy minima for both "reactant" and "product" as well as the "transition state"). In order for the walls to be effective, we also require that they are significantly higher than the expected reaction barrier (otherwise the likelihood to cross the wall during meta dynamics would be higher than that for the barrier). From the potential energy profile (static calculations not reported here) we obtained a reasonable guess for the reaction barrier - it is about 0.4 eV - hence the height for the wall of 1 eV should be sufficient. | In principle, meta dynamics always seeks for the path of least resistance. In the case of our model system this corresponds to the dissociation of the vdW complex (which is linked with a lower barrier than the SN2 reaction). In order to avoid this undesired process, an extra bias potential ("repulsive walls") is used whose role is to restrict our sampling to a relevant region (approx. <math>-3 \AA < </math> collective variable <math>< 3 A</math>). In fact, the positions of walls can be chosen arbitrarily - we only require that the region between the walls contains all the information we are interested in (in this case we want to see free-energy minima for both "reactant" and "product" as well as the "transition state"). In order for the walls to be effective, we also require that they are significantly higher than the expected reaction barrier (otherwise the likelihood to cross the wall during meta dynamics would be higher than that for the barrier). From the potential energy profile (static calculations not reported here) we obtained a reasonable guess for the reaction barrier - it is about 0.4 eV - hence the height for the wall of 1 eV should be sufficient. | ||
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 {{TAG|HILLSPOT}} file (containing bias potential generated in previous run) must be copied to the {{TAG|PENALTYPOT}} fiel (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 50 ] | |||
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 | |||
Please run this script by typing: | |||
bash ./run | |||
*Importantly the user has to adjust the runvasp variable, which holds the command for the executable command. | |||
*The calculation is run for 50 ps. For convenience the calculation is split into 50 calculations each of length 1 ps. | |||
== Download == | == Download == | ||
Revision as of 16:15, 26 September 2019
Task
In this example the nucleophile substitution of a Cl- by another Cl- in CH3Cl via meta dynamics is correctly simulated by using extra "repulsive potential walls."
Input
POSCAR
1.00000000000000
12.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 12.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 12.0000000000000000
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
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 ##############################################################################
- Same INCAR file as in the previous example (Nuclephile Substitution CH3Cl - mMD).
ICONST
R 1 5 0 R 1 6 0 S 1 -1 5
Calculation
In principle, meta dynamics always seeks for the path of least resistance. In the case of our model system this corresponds to the dissociation of the vdW complex (which is linked with a lower barrier than the SN2 reaction). In order to avoid this undesired process, an extra bias potential ("repulsive walls") is used whose role is to restrict our sampling to a relevant region (approx. collective variable ). In fact, the positions of walls can be chosen arbitrarily - we only require that the region between the walls contains all the information we are interested in (in this case we want to see free-energy minima for both "reactant" and "product" as well as the "transition state"). In order for the walls to be effective, we also require that they are significantly higher than the expected reaction barrier (otherwise the likelihood to cross the wall during meta dynamics would be higher than that for the barrier). From the potential energy profile (static calculations not reported here) we obtained a reasonable guess for the reaction barrier - it is about 0.4 eV - hence the height for the wall of 1 eV should be sufficient.
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 fiel (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 50 ] 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
Please run this script by typing:
bash ./run
- Importantly the user has to adjust the runvasp variable, which holds the command for the executable command.
- The calculation is run for 50 ps. For convenience the calculation is split into 50 calculations each of length 1 ps.