How to include Drude particles into the top file?

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Dear all,

I want to modify the .top file to use the Drude force field. When I look at the aminoacid.rtp from the Drude force field downloaded here:

[ 123TBB ]
[ atoms ]
; name type charge cgnr alpha thole
C1 CD2R6A 2.92049 0 0.002940 0.7600
DC1 DRUD -2.97549 1
H1 HDR6A 0.13000 2

There specifies the DRUD type for the the Drude particle (If I understand correctly).

Then to match the .top file which contains the Drude particle, I need to assign the Drude particle in the .gro file. (If I understand correctly)

My question is, how to assign the xyz coordinates for the Drude particle? Reasonably arbitrarily?

Many thanks in advance.

Drude oscillators should initially be constructed with identical coordinates as their parent atoms, and the dipoles subsequently allowed to relax via energy minimization.

Beware that the Drude implementation is still being actively developed and is not production-level software. It has only been through basic validation and does not support all features that other programs do.