[gmx-users] How can i know if the protein swell during the MD simulation?

[Tsjerk Wassenaar]

Hi,

Well, I think 'swelling' is unambiguously, though roughly, defined as
'growing larger', which suggests that you'd have to look for an
increase in volume. But how to do that, how to define the volume of
the protein is still a matter of setting your criteria and finding the
right tools to assess these. Not the simplest thing...

Cheers,

Tsjerk

On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Chih-Ying Lin wrote:
>>
>> HI
>> How can i know if the protein swell during the MD simulation?
>>
>> What are those indications to "see" the swollen protein?
>>
>
> How do you define the term "swelling?"  This again sounds like another issue
> on defining your own criteria for the expected behavior and reading the
> manual about available analysis tools.
>
> -Justin
>
>> Thank you
>> Lin
>>
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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