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.rete...@gmail.com> wrote: > sovent accesible surface area? > > On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: >> >> stretching != swelling, e.g. >> >> On Mon, May 18, 2009 at 10:46 AM, Bhanu <bhanui...@gmail.com> wrote: >> > How about checking radius of gyration??? >> > >> > 2009/5/18 Tsjerk Wassenaar <tsje...@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 <jalem...@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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> >> >> _______________________________________________ >> >> >> gmx-users mailing list gmx-us...@gromacs.org >> >> >> 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 gmx-users-requ...@gromacs.org. >> >> >> 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 gmx-us...@gromacs.org >> >> > 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 gmx-users-requ...@gromacs.org. >> >> > 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 gmx-us...@gromacs.org >> >> 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 gmx-users-requ...@gromacs.org. >> >> 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 gmx-us...@gromacs.org >> > 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 gmx-users-requ...@gromacs.org. >> > 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 gmx-us...@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
