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

[Tsjerk Wassenaar]

stretching != swelling, e.g.

On Mon, May 18, 2009 at 10:46 AM, Bhanu <bhanuiitr at gmail.com> wrote:
> How about checking radius of gyration???
>
> 2009/5/18 Tsjerk Wassenaar <tsjerkw at gmail.com>
>>
>> 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
>> F: +31-30-2537623
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>
>
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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
F: +31-30-2537623