[gmx-users] center of mass
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 9 09:27:35 CEST 2004
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.
> > 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.
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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
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