[gmx-users] RMSD analysis and stability

[Bratin Kumar Das]

You can see the radius of gyration, number of hydrogen bond, native contact
etc for assessing the stability

On Sun 15 Sep, 2019, 4:32 PM Quin K, <profiles.ke at gmail.com> wrote:

> Thank you!
> What else should I be looking for?
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> On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/15/19 5:30 AM, Quin K wrote:
> > > Hi everyone!
> > >
> > > I have done a MD simulation for a protein structure at 310K (100ns)
> this
> > is
> > > the RMSD at around 65 ns kindly comment on the stability. Will I have
> to
> > > rerun the MD?
> > > Kindly let me know how to decide stability by analyzing RMSD.
> >
> > RMSD alone is generally insufficient to make any definitive conclusions
> > about stability. I see nothing out of the ordinary in the plot.
> >
> > -Justin
> >
> > > For backbone
> > > <
> >
> https://drive.google.com/file/d/18JjiAKivbWklIXRSVaqhQ2zMUN9L_hkl/view?usp=sharing
> > >
> > > For backbone xvg file
> > > <
> >
> https://drive.google.com/file/d/12MBTO57f_xROW5mWTFtMskwTNL1gCvam/view?usp=sharing
> > >
> > > For protein
> > > <
> https://drive.google.com/file/d/1LrdIFxQ-rBrIkcgbnfgEHg424cKgGm7_/view>
> > > For protein - expanded
> > > <
> https://drive.google.com/file/d/1yvwLzdYMAenL9n1kOdaVzOo5JU6j4YU-/view>
> > > For protein xvg file
> > > <
> >
> https://drive.google.com/file/d/1hKbbTOCLqG7xDySQ7r4VcrNfSaokmYJO/view?usp=sharing
> > >
> > >
> > >
> > > Thank you in advance.
> > >
> > > Regards!
> > >
> > > <
> >
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> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
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> >
> > Virginia Tech Department of Biochemistry
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> > jalemkul at vt.edu | (540) 231-3129
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> >
> > ==================================================
> >
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