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

[Mark Abraham]

Hi Meena,

If you're going to use the digest, please don't reply to the digest. Start
a new email with a sensible subject line and respect your readers. :-)

Improper dihedrals are often used for keeping things planar, not just for
proper dihedrals of four consecutively bound atoms. See manual.

Mark

On Mon, Aug 3, 2015 at 2:15 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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*
>> > --
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