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

[Meena Singh]

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*