R: R: [gmx-users] Dihedral restraints

[STEVENAZZI ANDREA]

Dear David
I am desperate actually and would appreciate a lot if you could send me the dihres.c that works with version 3.2.
Just in case is not so clear how to add the right lines in the topology file by reading the code would you please suggest it to me too?
Thanks a lot
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
Tel: +39-02-64433097
-----Messaggio originale-----
Da: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Per conto di David Mobley
Inviato: giovedì 16 marzo 2006 0.59
A: Discussion list for GROMACS users
Oggetto: Re: R: [gmx-users] Dihedral restraints

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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