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

[Tsjerk Wassenaar]

Well, why didn't I think of that? Maybe because flattening will also
increase the SAS, or (partial) unfolding, or opening of two domains...

:)

Tsjerk

On Tue, May 19, 2009 at 6:10 PM, Marius Retegan
<marius.s.retegan at gmail.com> wrote:
> sovent accesible surface area?
>
> On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>>
>> 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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>>
>>
>> --
>> 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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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