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: [EMAIL PROTECTED] Tel: +39-02-64433097 -----Messaggio originale----- Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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 <[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 _______________________________________________ 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
