Hi Lin, Well, actually G53a6 is heavily reparameterized... partly. So your observation that large portions of the force fields are equal is correct. That also makes the question of whether or not to mix them more difficult. It seems implicitly assumed by the authors that the parts of the force field that weren't reparameterized are still compatible with the new parameters. Some of the things you do have to be aware of though is that aromatics have changed, charges have changed and non-nonded parameters have changed. If you want to use parameters from 45a3 in 53a6 for aromatic compounds, you should have a good look at what happened to similar compounds (residues) which were reparameterized. In summary, the advice is still: don't do it. First get on terms with force fields and parameterization. Maybe it's not even a bad idea to use 45a3 in stead.
Cheers, Tsjerk On Mon, May 11, 2009 at 3:47 PM, Chih-Ying Lin <chihying2...@gmail.com> wrote: > Hi > > GROMOS 45a3 force field > GROMOS 53a6 force field > Are they compatible? > > I notice that MOST of the force field parameters sets are THE SAME in the > GROMOS 45a3 and GROMOS 53a6. > > So, I want to ask if GROMOS 53a6 is rectification from GROMOS 45a3. > I mean if GROMOS 53a6 match more experimental data than GROMOS 45a3. > But, basically GROMOS 45a3 and GROMOS 53a6 are derived from THE SAME > METHOD and THE SAME EXPERIMENTAL DATA SETS ? > > Thank you very much > > 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 > -- 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
