From: Axel Kohlmeyer (
Date: Tue Apr 22 2008 - 14:32:07 CDT

On Tue, 22 Apr 2008, wrote:

RC> Hello Axel,
RC> the attached file is a simple Si10 cluster in which you can manually
RC> measure (through Mouse->Label->bonds) the nearest neighbour distance to
RC> be less or equal to 2.60 angstroms.

please re-run the g(r) analysis with a smaller interval size.
your case is _very_ borderline and depends on how you define
the r value that is plotted. the current output does not center
on the interval but prints the r up to which the g(r) is computed.
if you use a shorter interval, e.g. 0.01 you'll see that most of
your data got "rounded up" into the 2.7 bin (which is the 2.6 to 2.7
bin in practice).

you cannot take the label values as reference, since you don't
see whether you have 2.603 or 2.597. you are in so far correct
that numbers seem to get rounded up a little bit too much. but
the deltar=0.01 results look more reasonable.

RC> Now evaluate the g(r) and click on the highest point of the first peak;
RC> it is centered around 2.71 Angstroms instead of ~2.60.

please note that those numbers also depend a little bit on
where you have the cursor focus. just click multiple times
when moving the mouse a tiny bit and you'd see a difference.
the proper numbers you can only get when writing them to a file.


RC> On marted́ 22 aprile 2008, Axel Kohlmeyer wrote:
RC> > On Tue, 22 Apr 2008, wrote:
RC> >
RC> > RC> Hello,
RC> > RC>
RC> > RC> I noticed that the first peak of a g(r) calculation with the vmd
RC> > RC> extension is slightly shifted respect to the expected value.
RC> > RC> Check this out with a very well ordered structure (for example
RC> > RC> graphene).
RC> > RC> In my case (cristalline silicon nanoclusters) it gives 2.70
RC> > instead of RC> 2.43.
RC> > RC>
RC> > RC> Anyone confirms?
RC> >
RC> > no. the peaks are exactly where they should be in my tests.
RC> > e.g. in rigid spc/e water it get the intramolecular peak at
RC> > exactly 1. angstrom.
RC> >
RC> > please provide a coordinate/trajectory file that reproduces this,
RC> > explain how you obtained it, and with which code you get the
RC> > different g(r).
RC> >
RC> > thanks,
RC> > axel.
RC> >
RC> > RC>
RC> > RC> Thanx,
RC> > RC> Rob.
RC> > RC>

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.