[gmx-users] center of mass

[David van der Spoel]

On Wed, 2004-06-09 at 05:36, Qi Sun wrote:
> At 09:09 AM 6/9/2004 +1000, you wrote:
> > > consider the whole molecule as single super atom. Right now the
> > > index file can consider each atoms as separate points, I am more
> > > interested in the whole molecule together. Is there a algorithm
> > > somewhere can solve this problem?
> > 
> > Is there a central atom that you can chose to be the of the entire
> > molecule and measure the RDF from that?
> 
> Thanks for your comments. Your idea is definitely right for some
> molecules like N,N-dimethyl-formamide, I will use the N atoms as the
> center of the whole molecules as you suggested. For another solvent in
> my system: Cyclohexane with a cyclic structure is impossible to find a
> atom at the center. 
checkout g_sorient
> 
> > Catch ya,
> > 
> > Dr. Dallas Warren
> > Research Fellow
> > Department of Pharmaceutical Biology and Pharmacology
> > Victorian College of Pharmacy, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9083
> > --------------------------------------------------------------------------
> > When the only tool you own is a hammer, every problem begins to
> > resemble a nail.
> > _______________________________________________
> > 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.
> 
> 
> 
> ______________________________________________________________________
> _______________________________________________
> 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.
-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++