Greetings
I'm trying to use the drude forcefield in gromacs for a small alcohol molecule.I tried to follow the topology of aminoacid as an example. I put drude particules in every Carbon atom and Oxygen. Also two virtual sites in the vicinity of the Oxygen atom. I didnt put the thole parameters because I dont know how it goes so I leave as a comment (;) as this:
[ atoms ]
; nr type resnr resid atom cgnr charge mass alpha thole
1 CD33A 1 MIB C 1 +2.30823 11.61100 ;0.002051 1.30
2 DRUD 1 MIB DT 1 -2.48523 0.40000
3 HDA3A 1 MIB H 1 +0.05900 1.00800
4 HDA3A 1 MIB H 1 +0.05900 1.00800
5 HDA3A 1 MIB H 1 +0.05900 1.00800
6 CD31A 1 MIB C 2 +1.88511 11.61100 ;0.001302 1.30
7 DRUD 1 MIB DT 2 -1.98011 0.40000
...
Nevertheless it failed at the minimization step.
Is there an file example for small molecules with polarization in gromacs, or how to include the thole parameters?
kind regards
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