How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar <[email protected]>
> 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 <[email protected]> > 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 > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to [email protected]. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > > ======================================== > > > > 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 > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > 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 [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love.... they maybe the reason your heart aches today... but they are definitely the reason your heart beats.... : COPIED FROM GMAIL CUSTOM MSGS.
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