Hi Pascal, Please specify the (Gromos) force field used further. There seems to be something with the 53a5/6 series in terms of alpha helix / beta sheet preference. I'm not sure whether this has been fixed already. I don't recall having heard of such an issue with the 43a2/45a3 series. But these have there own problems of course, just as any force field has. Keep up the development!
Anyway, hope this is useful to you. Cheers, Tsjerk On Feb 20, 2008 5:41 PM, <[EMAIL PROTECTED]> wrote: > > Hi everybody, > > I am doing some protein unfolding simulations and getting some new, compact > and > beta-sheet rich unfolded states.I have read 2-3 papers comparing force fields > and suggesting that the gromos force field might overstabilize beta-sheets. > Has > anybody else obtained beta -rich unfolded conformations in protein unfolding > simulations, or know of any other relevant reference I might have overseen? > > Thanks a lot in advance!! > > Pascal > > > ******************************************************************************* > Pascal Baillod (PhD student) > ******************************************************************************* > Swiss Federal Institute of Technology EPFL Tel: > +41-(0)21-693-0322 > Institute of Chemical Sciences and Engineering , Fax: > +41-(0)21-693-0320 > Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED] > Room BCH 4121, Avenue Forel, > http://lcbcpc21.epfl.ch > CH-1015 Lausanne > ******************************************************************************* > _______________________________________________ > 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
