[gmx-users] restraining to center of geometry?

Dr. Christoph Freudenberger christoph.freudenberger at ch.tum.de
Mon Jan 26 10:04:01 CET 2004


Possibly exactly what you think of, but maybe you can define
a dummy that points at least approx. to your desired position
and use that for disre or posre.

Michael Shirts wrote:
> Hello, all-
> So, supposing I had a protein, and wanted to restrain a ligand by attaching
> it with a spring to some point that wasn't actually an atom -- say it was
> the center of geometry of a number of atoms around the binding pocket, so that
> it's a point that redefines itself at each step of the simulation.
> 1) Is this possible to do using either the position restraint or distance
> restraint tools in GROMACS?
> 2) If not, how might one modify the code to put this in?
> Thanks,
> Michael Shirts
> Stanford University.
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Dr. Christoph Freudenberger
Institut fuer Organische Chemie and Biochemie II
Technische Universitaet Muenchen
Lichtenbergstr. 4
D-85747 Garching, Germany

Tel.: ++49 (0)89 289 13313
Fax.: ++49 (0)89 289 13210
email: Christoph.Freudenberger at ch.tum.de

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