Example: Importing conformers into PES explorations¶

#!/bin/sh


# Step 1: Run the conformer tool to quickly get a set of minima on the PES
# ------------------------------------------------------------------------

$AMSBIN/conformers << EOF

Generator
   RDKit
      InitialNConformers 100
   End
End

System
    Atoms
        N -1.912873733399416 2.022897940092991 -0.1378294583620503
        C -0.871664156578182 3.02960778940094 0.06584379364356192
        C 0.5013812000791015 2.352115382193892 0.0410146984615521
        O 0.812167345172201 1.847076794564962 -1.240836870209463
        H -1.850257440384896 1.675835972092315 -1.088966428216949
        H -2.82010628990089 2.459772455658122 -0.02412199180453132
        H -1.024866752021569 3.492408399687411 1.045420209976512
        H -0.9134720948542179 3.809309747393572 -0.7093004343600406
        H 0.5270488401868264 1.547182041972351 0.7934160458635944
        H 1.275876827761384 3.088526288396493 0.2854207086154862
        H 0.2041922851100986 1.132993293447435 -1.463777763138591
    End
    BondOrders
         1 2 1.0
         1 5 1.0
         1 6 1.0
         2 3 1.0
         2 7 1.0
         2 8 1.0
         3 4 1.0
         3 9 1.0
         3 10 1.0
         4 11 1.0
    End
End

Engine DFTB
   Model DFTB0
   ResourcesDir DFTB.org/mio-1-1
EndEngine

RNGSeed 20200512 # Just to make the test output deterministic ...

EOF


# Step 2: Import energy landscape by running a LandscapeRefinement on it
# ----------------------------------------------------------------------
#
# The energy landscape that is produced by the conformers tool does not contain
# the engine output files of the individual states, which contain e.g. the
# normal modes. It can be used as input to the PESExploration ->
# LandscapeRefinement job, but not for the other PESExploration jobs (e.g.
# ProcessSearch). You should therefore always run the conformers output through
# a quick LandscapeRefinement before proceeding to other PES exploration jobs.
#
# At this point you can also trim down the number of minima loaded from the set
# of conformers. In the example below, we only load the 10 lowest energy
# conformers.


AMS_JOBNAME=refinement $AMSBIN/ams << EOF

Task PESExploration

PESExploration
   Job LandscapeRefinement
   LoadEnergyLandscape
     Path conformers.results/conformers.rkf
     KeepOnly 1:10
   End
End

Engine DFTB
   Model DFTB0
   ResourcesDir DFTB.org/mio-1-1
EndEngine

RNGSeed 20200512 # Just to make the test output deterministic ...

EOF


# Step 3: Run a process search around the lowest energy conformer
# ---------------------------------------------------------------
#
# We load all states we got from the LandscapeRefinement and run a single
# expedition around the lowest energy conformer. This will give us a set of
# transition states connecting it to other conformers, but possibly also other
# isomers.


AMS_JOBNAME=process_search $AMSBIN/ams << EOF

Task PESExploration

PESExploration
   Job ProcessSearch
   LoadEnergyLandscape
     Path refinement.results
     SeedStates 1
   End
   DynamicSeedStates False
   NumExpeditions 1
   NumExplorers 64
End

LoadSystem
   File refinement.results/ams.rkf
End

Engine DFTB
   Model DFTB0
   ResourcesDir DFTB.org/mio-1-1
EndEngine

RNGSeed 20200512 # Just to make the test output deterministic ...

EOF

# Note that DFTB0 wrongly predicts an energetically favorable proton transfer
# from the OH group to the NH2 group. This would not have happened if we had
# used SCC-DFTB, but it is a nice example to show off the input for these jobs
# and that the PES exploration can discover also isomers, while the conformer
# tool should only produce conformers.