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

[Mark Abraham]

Hi,

As you have seen "parameters for nitrate" might depend on the application.
Those suitable for perhaps aqueous solvation are not necessarily useful for
coordination to a metal.

And also check out
http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software
comments about rendered bonds. If your topology didn't specify a bond,
GROMACS can't make it ;-)

Mark

On Mon, Aug 3, 2015 at 11:41 AM Aishwary Shivgan <
aishwaryshivgan55 at gmail.com> wrote:

> 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*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>