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 <[EMAIL PROTECTED]> 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 manual is a bit outdated.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: [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]> > >> Tel: +39-02-64433097 > >> > >> > >> > >> > >> > > ------------------------------------------------------------------------ > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
