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,
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aromatic groups from an unpublished paper from the Van Gusteren group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
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