[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

[Tsjerk Wassenaar]

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 <chihying2008 at 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-users at 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-request at 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