SV: Re: [gmx-users] constraint distance

[David Mobley]

Allow me to take this opportunity to reiterate that the ability to
only apply distance/angle/dihedral restraints between atoms in the
same "molecule" (in the topology sense) is really lame. It would be
really nice if GROMACS could handle absolute atom numbering for
restraints (i.e. using the numbering as in the .gro file rather than
in the topology file).

David


On 9/11/06, Soren Enemark <blegbirk at yahoo.dk> wrote:
>
>
> David van der Spoel <spoel at xray.bmc.uu.se> skrev:
>  Soren Enemark wrote:
> > Hi,
> > maybe I am misunderstanding either the manual or the topic.. but - in
> > my world -
> > I never stop being puzzled by the part of chapt 6 in the manual which
> > apparently
> > says that such distance constraining is possible even though it (seems)
> > to be
> > secretly known that it is _not_ possible unless one uses the method
> > suggested
> > below.
> > I believe, I suggest adding a comment in the manual.
> >
>
> can you be more specific which part of the manual you mean?
>
>  Basically almost anywhere in chapter 6 from 6.1 to 6.25 included.
>
>  I mean, pulling works between 2 different molecules, why is it then obvious
> that constraining doesn't?
>
>
>
> > -Soren
> >
> > */Tsjerk Wassenaar /* skrev:
>
> >
> > Hi Kanin,
> >
> > The only way to get away with that is to merge your two parts to form
> > one molecule, with the only connection being a distance_restraint (or
> > another bonded term if you want to emulate bond-like behaviour such as
> > a salt-bridge).
> >
> > Best,
> >
> > Tsjerk
> >
> > On 9/11/06, kanin wichapong wrote:
> > > Dear All
> > > I would like to know how to constraint the distance between the
> > > different molecule, ex. the ligand and the protein. As far as I know
> > > whatever to do the constraint, distance, angle dihedral, it can
> > do just in
> > > the same molecule.
> > > Thank you in advance for all of your help.
> > >
> > > With Best all regard,
> > > Kanin
> > >
> > > _______________________________________________
> > > 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
> > >
> > >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> > Dept. of Biophysical Chemistry
> > University of Groningen
> > Nijenborgh 4
> > 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> > _______________________________________________
> > 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
> >
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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.
> ________________________________________________________________________
> 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
> 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
>
>
> _______________________________________________
> 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
>
>