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

[Bhanu]

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
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> The Netherlands
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