GROMACS version:git version
GROMACS modification: No
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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:http://mackerell.umaryland.edu/charmm_drude_ff.shtml
[ 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.