Example: The role of specifying the atom types

Now we look at a Propanenitrile molecule, the QM region is highlighted.

../_images/Propanenitrile.png

We run this with and without specifying the atom types on input. In principle this makes a difference for the MM type for atom “C(3)” in the MM sub calculation on atoms 3,7,8, and 9. If specified it will be C_3 (as it is in the whole Propanenitrile molecule), but if not it will be guessed as C_R. In practice there is no effect for this calculation.

Let us have a look at the report generated by the example, that pretty much explains what is done

Download report Propanenitrile.txt


We first check how bad the MM method is compared to the QM method for some distances in the QM region

Here are the distances (Angstrom) as obtained with a QM and an MM method
  distance         qm         mm    err(mm)
 C(1)-C(2)      1.456      1.467      0.011
 C(1)-N(4)      1.147      1.157      0.010
 C(2)-H(5)      1.095      1.110      0.015

Can we get better results for the QM region with the hybrid engine?

Even though UFF has automatic atom typing, it still matters (in principle) whether we specify it on input or not
  * Without typing for each region the types are automatically guessed
  * With typing the types are always as on input (for all regions)

The only difference is in the C type for the MM region.

Here are the distances (Angstrom) as obtained with a QM and an Hybrid method without explicit typing
  distance         qm     hybrid err(hybrid)
 C(1)-C(2)      1.456      1.456      0.000
 C(1)-N(4)      1.147      1.147      0.000
 C(2)-H(5)      1.095      1.092     -0.003

Here are the distances (Angstrom) as obtained with a QM and an Hybrid method with explicit typing
  distance         qm     hybrid err(hybrid)
 C(1)-C(2)      1.456      1.456      0.000
 C(1)-N(4)      1.147      1.147      0.000
 C(2)-H(5)      1.095      1.092     -0.003

Here are some observations for this example
     * The hybrid engine does better than pure MM
     * The subtle issue whether or not we specify the types has negligible effect.

Download Propanenitrile.run

#!/bin/sh

export NSCM=1


for engine in dftb forcefield
do

export AMS_JOBNAME=$engine

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

System
    Atoms
        C -0.02116 1.01286 0.0 region=qm
        C 0.01258 -0.45034 0.0 region=qm
        C 1.44394 -1.0175 0.0 
        N -0.03362 2.17616 0.0 region=qm
        H -0.54281 -0.80179 0.88302 region=qm
        H -0.54281 -0.80179 -0.88302 region=qm
        H 1.40659 -2.11445 0.0 
        H 1.99584 -0.68766 -0.88907 
        H 1.99584 -0.68766 0.88907 
    End
    GuessBonds true
End

Engine $engine
EndEngine
eor

done

report=report.txt

printf "\nWe first check how bad the MM method is compared to the QM method for some distances in the QM region\n" > $report

bond1="C(1)-C(2)"
bond2="C(1)-N(4)"
bond3="C(2)-H(5)"
bond4="C(2)-C(3)"

aaa1qm=`$AMSBIN/amsreport dftb.results/dftb.rkf -r distance#1#2`
bbb1qm=`$AMSBIN/amsreport dftb.results/dftb.rkf -r distance#1#4`
ccc1qm=`$AMSBIN/amsreport dftb.results/dftb.rkf -r distance#2#5`
ddd1qm=`$AMSBIN/amsreport dftb.results/dftb.rkf -r distance#2#3`


aaa1mm=`$AMSBIN/amsreport forcefield.results/forcefield.rkf -r distance#1#2`
bbb1mm=`$AMSBIN/amsreport forcefield.results/forcefield.rkf -r distance#1#4`
ccc1mm=`$AMSBIN/amsreport forcefield.results/forcefield.rkf -r distance#2#5`
ddd1mm=`$AMSBIN/amsreport forcefield.results/forcefield.rkf -r distance#2#3`

errmma=`echo "$aaa1mm- $aaa1qm" | bc`
errmmb=`echo "$bbb1mm- $bbb1qm" | bc`
errmmc=`echo "$ccc1mm- $ccc1qm" | bc`
errmmd=`echo "$ddd1mm- $ddd1qm" | bc`


printf "\nHere are the distances (Angstrom) as obtained with a QM and an MM method\n" >> $report
printf "%10s %10s %10s %10s\n"   "distance"  "qm"  "mm" "err(mm)">> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond1  $aaa1qm $aaa1mm $errmma >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond2  $bbb1qm $bbb1mm $errmmb >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond3  $ccc1qm $ccc1mm $errmmc >> $report

printf "\nCan we get better results for the QM region with the hybrid engine?\n" >> $report

printf "\nEven though UFF has automatic atom typing, it still matters (in principle) whether we specify it on input or not\n" >> $report

printf "  * Without typing for each region the types are automatically guessed\n" >> $report
printf "  * With typing the types are always as on input (for all regions)\n" >> $report
printf "\nThe only difference is in the C type for the MM region.\n" >>$report


export AMS_JOBNAME=hybrid.types=no

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

System
    Atoms
        C -0.02116 1.01286 0.0 region=qm
        C 0.01258 -0.45034 0.0 region=qm
        C 1.44394 -1.0175 0.0 
        N -0.03362 2.17616 0.0 region=qm
        H -0.54281 -0.80179 0.88302 region=qm
        H -0.54281 -0.80179 -0.88302 region=qm
        H 1.40659 -2.11445 0.0 
        H 1.99584 -0.68766 -0.88907 
        H 1.99584 -0.68766 0.88907 
    End
    GuessBonds true
End

Engine Hybrid
    QMMM qmRegion=qm qmEngineID=dftb mmEngineID=forcefield

    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

EndEngine

eor


aaa1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#1#2`
bbb1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#1#4`
ccc1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#2#5`
ddd1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#2#3`

errhybrida=`echo "$aaa1hybrid- $aaa1qm" | bc`
errhybridb=`echo "$bbb1hybrid- $bbb1qm" | bc`
errhybridc=`echo "$ccc1hybrid- $ccc1qm" | bc`
errhybridd=`echo "$ddd1hybrid- $ddd1qm" | bc`


printf "\nHere are the distances (Angstrom) as obtained with a QM and an Hybrid method without explicit typing\n" >> $report
printf "%10s %10s %10s %10s\n"   "distance"  "qm"  "hybrid" "err(hybrid)">> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond1  $aaa1qm $aaa1hybrid $errhybrida >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond2  $bbb1qm $bbb1hybrid $errhybridb >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond3  $ccc1qm $ccc1hybrid $errhybridc >> $report


export AMS_JOBNAME=hybrid.types=yes

rm -rf $AMS_JOBNAME.results

"$AMSBIN/ams" << eor

Task GeometryOptimization

System
    Atoms
        C -0.02116 1.01286 0.0       region=qm
        C 0.01258 -0.45034 0.0       region=qm
        C 1.44394 -1.0175 0.0        region=mm
        N -0.03362 2.17616 0.0       region=qm
        H -0.54281 -0.80179 0.88302  region=qm
        H -0.54281 -0.80179 -0.88302 region=qm
        H 1.40659 -2.11445 0.0       region=mm
        H 1.99584 -0.68766 -0.88907  region=mm
        H 1.99584 -0.68766 0.88907   region=mm
    End
    GuessBonds true
    LoadForceFieldAtomTypes File=forcefield.results
End

Engine Hybrid
    QMMM qmRegion=qm qmEngineID=dftb mmEngineID=forcefield

    Engine DFTB
    EndEngine

    Engine ForceField
    EndEngine

EndEngine

eor

aaa1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#1#2`
bbb1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#1#4`
ccc1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#2#5`
ddd1hybrid=`$AMSBIN/amsreport $AMS_JOBNAME.results/hybrid.rkf -r distance#2#3`

errhybrida=`echo "$aaa1hybrid- $aaa1qm" | bc`
errhybridb=`echo "$bbb1hybrid- $bbb1qm" | bc`
errhybridc=`echo "$ccc1hybrid- $ccc1qm" | bc`
errhybridd=`echo "$ddd1hybrid- $ddd1qm" | bc`


printf "\nHere are the distances (Angstrom) as obtained with a QM and an Hybrid method with explicit typing\n" >> $report
printf "%10s %10s %10s %10s\n"   "distance"  "qm"  "hybrid" "err(hybrid)">> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond1  $aaa1qm $aaa1hybrid $errhybrida >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond2  $bbb1qm $bbb1hybrid $errhybridb >> $report
printf "%10s %10.3f %10.3f %10.3f\n"   $bond3  $ccc1qm $ccc1hybrid $errhybridc >> $report

printf "\nHere are some observations for this example\n" >>$report
printf "     * The hybrid engine does better than pure MM\n" >>$report
printf "     * The subtle issue whether or not we specify the types has negligible effect.\n" >>$report

echo "begin report"
cat $report
echo "end report"