[gmx-users] Nitrate ion doesnt remain planar after md run

[Aishwary Shivgan]

I think you need to use improper dihedrals to keep oxygen atoms in plane.

On Mon, Aug 3, 2015 at 1:54 PM, Meena Singh <meenadcat at gmail.com> wrote:

> Dear GROMACS users,
>
> I am doing MD simulation of metal ion with nitrate ion in aqueous phase and
> I am using OPLS forcefield. Partial charges and potential parameters have
> been taken from research paper.
>
> But after production MD run all three oxygens of nitrate
> are coordinating with metal ion, but nitrate is bidentate ligand.
>
> I also observed that nitrate is not planar (I have specified bond angle 120
> in parameters) and there are false bonds between the O's of nitrate, I mean
> there are bond between O-O of nitrate. Seems like nitrate's O is getting
> fused among themselves.
>
> Please help me out with my problem.
>
> Thank you
> --
> *Regards,*
> *Meena Singh*
> *Ph. D. Research Scholar*
>
> *Chem Engg Dept,*
>
> *Institute of Chemical Technology, Mumbai*
> --
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