This has got nothing to do with Gromacs.
A general comment: no, you should not neglect it. I am not sure what you
mean by "QM," but the total charge of the system calculated by either
DFT, or with Hartree-Fock, is _imposed_ and is not the result of
calculations -- this sets up the sanity check for the density
distribution. If you set up your QM calculations by demanding that the
total charge is zero and the result is nonzero, you probably screwed
something up with boundaries, basis sets, spin multiplicity, etc, etc,
so the result is not trustworthy. Obtaining MD parameters from quantum
chemistry is a whole field in itself.
Alex
On 6/1/2018 12:49 AM, rose rahmani wrote:
Hi,
I used QM for calculating atoms partial charges for ZnS nanotube but it has
totally -0.04 charge. I want to study the interaction of this nanotube with
some biomolecules by AMBER99SB force field.
Is it wrong to calculate these interaction in presence of -0.04 charge by
this force field? Should i neglect it?
Would you please help me or give me a suggestion?
Best regards
--
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