[gmx-users] Restraints of COM 2

Eudes Fileti fileti at ufabc.edu.br
Mon Apr 5 15:04:20 CEST 2010

Hello everybody, I have two benzene molecules and I want to restrain them
only by their center of mass. The conversation below (between Shirts and
Spoel) gave me some ideas but still I couldnt solve the problem. In
particular I'm not seeing any way to create this user group, nor how to
calculate its center of mass. Could someone give me a hand with that?

On Sun, 2004-01-25 at 04:00, Michael Shirts wrote:
> Hello, all-
> So, supposing I had a protein, and wanted to restrain a ligand by
> 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
> 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?
If this is dynamic, like the centre of mass of a group, you might add
something using a user group. Compute the center of mass of your user
group and call the position restraint routine. The good thing (TM) is
that you don't have to program any I/O.

> Thanks,
> Michael Shirts
> Stanford University.
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
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