[gmx-users] RMSD analysis and stability

[Justin Lemkul]

On 9/15/19 7:27 AM, Bratin Kumar Das wrote:
> You can see the radius of gyration, number of hydrogen bond, native contact
> etc for assessing the stability

Overall, "stability" implies persistence of important interactions 
(really it implies knowledge of free energy of the system, but 
structural metrics can be reasonable proxies). This may encompass native 
contacts (though how one defines "native" may be somewhat difficult to 
do), hydrogen bonds, and other interactions. For a globular protein, 
radius of gyration is not generally useful.

-Justin

> 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?
>> [image: mailcastr branding] Sent with Mailcastr
>> <
>> https://mailcastr.com/?utm_source=chrome-extension&utm_medium=branded-email&utm_campaign=BRANDING
>> 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!
>>>>
>>>> <
>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>>>> Virus-free.
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>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Office: 301 Fralin Hall
>>> Lab: 303 Engel Hall
>>>
>>> Virginia Tech Department of Biochemistry
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==================================================