[gmx-users] Nitrate ion doesnt remain planar after md run
aishwaryshivgan55 at gmail.com
Mon Aug 3 11:41:36 CEST 2015
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
> *Meena Singh*
> *Ph. D. Research Scholar*
> *Chem Engg Dept,*
> *Institute of Chemical Technology, Mumbai*
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