[gmx-users] RMSD analysis and stability

[Justin Lemkul]

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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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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