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

Meena Singh meenadcat at gmail.com
Mon Aug 3 10:24:46 CEST 2015

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*

More information about the gromacs.org_gmx-users mailing list