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

[Marius Retegan]

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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> >
> >
> >
> > --
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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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> Please search the archive at http://www.gromacs.org/search before posting!
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