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 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? 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. ________________________________________________________________________ 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 +55.11.4996-0196 http://fileti.ufabc.edu.br
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