sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar <[email protected]>wrote:
> stretching != swelling, e.g. > > On Mon, May 18, 2009 at 10:46 AM, Bhanu <[email protected]> wrote: > > 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. > > > > _______________________________________________ > > 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 >
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