patrick fuchs wrote:
Hi David,
since updated GROMOS force fields are now available within GROMACS, I
agree one does not need to use ffgmx, at least for standard simulations.
The only problem is for lipid/protein simulations. The only publicly
available I know that runs under GROMACS is the combination of Berger
lipids with ffgmx (on the website of Peter Tieleman). For someone
starting a project of lipid/protein simulations, there is a priori no
other public alternative (using GROMACS), although I know some new
parameters are about to be published.
Cheers,
But the Berger et al force field is based upon OPLS, and hence it can be
combined with OPLS all atom FF.
Patrick
David van der Spoel a écrit :
Reay, Andrew wrote:
Hi,
I am trying to find out why the Gromacs force field is no longer
recommended for use. I've searched the mailing list archives for
quite awhile to find the discussion but have been unsuccessful. Can
anybody tell me where to find that discussion? Thanks very much.
The never has bee a GROMACS force field, although we named it such to
avoid confusion with official "GROMOS" force fields. What used to be
called the GROMACS force field was basically GROMOS87 + changes due to
Van Buuren & Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on
aromatic groups from an unpublished paper from the Van Gusteren group
(these parameters are given in my paper in J.Biomol. NMR 8 (1996)
p.229). This is described in the manual. In other words there is no
good description of ths force field in a single paper. For good
reasons the Van Gunsteren group have updated their GROMOS force field
on a number of occasions, and these force field are now supported in
GROMACS, along with a few others. Although it is still possible to use
the old parameter set, please do not call it "The GROMACS force
field", but use the description above. Most referees fro scientific
papers will (should) raise their eyebrows when reading that this
parameter set was used, so this is another reason to shy away from it.
Andy
_______________________________________________
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
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
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
