R: [gmx-users] Dihedral restraints

[David Mobley]

Regarding dihedral restraints in 3.2, the dihres.c section of code
only was a placeholder in 3.2 (it printed out "dihedral restraints on"
but the dihedral restraints did nothing) but was fixed (sort of)
before release of 3.3. I think the forces were still wrong in t he 3.3
release, though, so even if you get 3.3 working, you will probably
need to get the fixed dihres.c.

I do, however, probably have a dihres.c floating around somewhere that
would work properly with 3.3, and possibly also with 3.2 (at one point
David van der Spoel wrote the section of code after I discovered it
was missing from the 3.2 release). If you are desperate I can dig
around for it.

Thanks,
David


On 3/15/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> STEVENAZZI ANDREA wrote:
> > Dear David
> > I did check the mailing list archives and could not find anything
> > related to.
> > Moreover, I have experienced some problems with version 3.3 of Gromacs
> > related to PME (see the mailing list archives) and I was forced to
> > install the 3.2.1 version in order to run a simulation.
> There is a workaround for this too on the ftp site.
>
> > So you are telling me that dihedral restraints can not be set up in the
> > 3.2 version?
> Don't recall but probably not.
>
> > I beg you pardon if these are stupid questions, but I have started to
> > use Gromacs just 2 weeks ago.
> > Thanks
> > Andrea
> >
> >
> >
> > STEVENAZZI ANDREA wrote:
> >> Dear Gromacs Users
> >>
> >> I am trying to use Gromacs for the MD of a small modified peptide
> > (just
> >> 4 residues with one ethylated) and I would like to set up one dihedral
> >
> >> restraint in the topology file.
> >>
> >> I have not found anything useful on the paper manual regarding
> > dihedral
> >> restraints and thought that it might not be possible to set them.
> >>
> >> However, analysing the mdout.mdp file I realised that the keyword
> > dihre
> >> (dihedral angle restraints) is actually there and can be turned on.
> >>
> >> If that is true, does anybody know the right lines to insert in the
> >> topology file in order to set properly a dihedral restraints?
> >>
> >> Thanks
> >
> >
> > manual is a bit outdated. check mailing list archives. it is possible
> > with 3.3
> >> Best regards
> >>
> >> Andrea
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Andrea Stevenazzi
> >>
> >> Medicinal & Computer Chemistry
> >>
> >> Italfarmaco Research Centre
> >>
> >> Italfarmaco SpA
> >>
> >> Via dei Lavoratori 54
> >>
> >> 20092 Cinisello Balsamo
> >>
> >> Milan
> >>
> >> E-mail: a.stevenazzi at italfarmaco.com
> > <mailto:a.stevenazzi at italfarmaco.com>
> >> Tel: +39-02-64433097
> >>
> >>
> >>
> >>
> >>
> > ------------------------------------------------------------------------
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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