Author Topic: Dummy atoms and COSMO - any changes from 2019?  (Read 4435 times)


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Dummy atoms and COSMO - any changes from 2019?
« on: May 30, 2023, 03:35:05 PM »
I am aware that it was not possible to use dummy atoms in combination with COSMO in Turbomole. However, I need to do a relaxed potential energy scan in a solvent
and what needs to be frozen is a dihedral angle at a spiro-atom centre (namely N-Cu-N plane with respect to P-Cu-P plane in a heteroleptic cuprous complex with
two chelate ligands). I see no easy way to freeze this dihedral other than using a dummy atom placed right in between the nitrogen atoms (or the phosphorus atoms, does
not matter). The Cu-dummy axis is then the convenient rotation axis of the P-Cu-P plane.

The question is, whether in the latest issues of Turbomole it has been made possible to use a dummy atom with some arbitrary (preferably small) radius that would have little
effect on the cavity shape and the results of the COSMO calculations.

I tried to place the radius for q in the COSMO section of the control file, but to no avail. The calculations would not run. Perhaps there is some clever way around this problem?

Marcin Andrzejak


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Re: Dummy atoms and COSMO - any changes from 2019?
« Reply #1 on: May 30, 2023, 05:26:54 PM »

did you try not to set q as atom type, but e.g. h (hydrogen), assign it no mass, no charge and no basis set?
Then assign a small radius to this atom only.

Say you have an input with 36 atoms and add a hydrogen which should act as dummy atom (obviously it will be atom number 37), so your $coord section has one more line.
Then, in $atoms, extend this keyword and add a few lines to define this new atom:

Code: [Select]
    basis = def-SV(P)
    jbas  = def-SV(P)
# next lines added manually:
h  37
    basis =none
    charge=  0.0
    mass  =  0.0

Hydrogen atom with number 37 is set up such that it has no basis set, no nuclear charge and no mass.
The rest of the atoms have def-SV(P) basis set assigned. Please note that the input shown here is the 'simple input' style which is available in newer Turbomole versions (introduced in version 7.5 from 2020), but can be used with the old style in a similar way.

Then, in $cosmo_atoms section, just add a small radius for this atom too:

Code: [Select]
# radii in Angstrom units
c  1-11,19-29                                                                  \
   radius=  2.0000
h  12-18,30-36                                                                 \
   radius=  1.3000
# new line added:
h  37   \
   radius= 0.1

Internal coordinates can make use of this atom as usual, but without basis set, charge and mass it will have no impact on the results (unless you place it in space such that it does change the cavity shape...).


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Re: Dummy atoms and COSMO - any changes from 2019?
« Reply #2 on: May 31, 2023, 10:29:29 AM »
Thank you very much indeed. This should work! I am trying it right away :)

Yours truly
Marcin Andrzejak