[gmx-users] RMSD analysis and stability

[Quin K]

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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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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