[gmx-users] gromacs.org_gmx-users Digest, Vol 136, Issue 6

[Meena Singh]

Thanks Aishwary Shivgan, but for specifying dihedral angles there should be
4 atom bonded consecutively, while in nitrate there are no dihedrals
angles.
Please let me know if I am wrong.

On Mon, Aug 3, 2015 at 3:30 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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>    1. Re: Nitrate ion doesnt remain planar after md run
>       (Aishwary Shivgan)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 3 Aug 2015 15:11:33 +0530
> From: Aishwary Shivgan <aishwaryshivgan55 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Nitrate ion doesnt remain planar after md run
> Message-ID:
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> 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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> End of gromacs.org_gmx-users Digest, Vol 136, Issue 6
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-- 
*Regards,*
*Meena Singh*
*Ph. D. Research Scholar*

*Chem Engg Dept,*

*Institute of Chemical Technology, Mumbai*