<div>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?</div>
<div><br></div><div>On Sun, 2004-01-25 at 04:00, Michael Shirts wrote:</div><div>> Hello, all-</div><div>> </div><div>> So, supposing I had a protein, and wanted to restrain a ligand by attaching</div><div>> it with a spring to some point that wasn't actually an atom -- say it was</div>
<div>> the center of geometry of a number of atoms around the binding pocket, so that</div><div>> it's a point that redefines itself at each step of the simulation.</div><div>> </div><div>> 1) Is this possible to do using either the position restraint or distance</div>
<div>> restraint tools in GROMACS?</div><div>> </div><div>> 2) If not, how might one modify the code to put this in?</div><div>If this is dynamic, like the centre of mass of a group, you might add</div><div>something using a user group. Compute the center of mass of your user</div>
<div>group and call the position restraint routine. The good thing (TM) is</div><div>that you don't have to program any I/O.</div><div><br></div><div>> </div><div>> Thanks,</div><div>> Michael Shirts</div><div>
> Stanford University.</div><div>-- </div><div>David.</div><div>________________________________________________________________________</div><div>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,</div>
<div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, <span class="Apple-tab-span" style="white-space:pre"> </span>75124 Uppsala, Sweden</div><div>phone:<span class="Apple-tab-span" style="white-space:pre"> </span>46 18 471 4205<span class="Apple-tab-span" style="white-space:pre"> </span>fax: 46 18 511 755</div>
<div>spoel at <a href="http://xray.bmc.uu.se">xray.bmc.uu.se</a><span class="Apple-tab-span" style="white-space:pre"> </span>spoel at <a href="http://gromacs.org">gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a></div>
<div>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</div>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>Santo André - SP - Brasil<br>CEP 09210-971<br>+55.11.4996-0196<br><a href="http://fileti.ufabc.edu.br">http://fileti.ufabc.edu.br</a><br>