R: [gmx-users] Dihedral restraints
dmobley at gmail.com
Thu Mar 16 00:59:18 CET 2006
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.
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 manual is a bit outdated.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
> > ------------------------------------------------------------------------
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> 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
> 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
> gmx-users mailing list gmx-users at gromacs.org
> 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
More information about the gromacs.org_gmx-users