[note: multiple copies of the same message to the reflector are
discouraged]
> I calculated the radial distribution functions, g(r), of the solvent
> (water TIP3P) with respect to
> every atom of each residue of my peptide (from 0.0 Angs up to 6.0
> Angs), with the following
> command:
>
> radial "name" 0.1 6.00 :WAT :"res"
...
> What I can not understand is why for few residues the value of the
> g(r) initial plateau is
> not zero but higher (for instance ~0.13 or ~0.2).
> I would expect that every initial plateaus is at zero, as atoms have
> finite dimensions.
The radial command uses the standard ptraj routines to calculate distance
and they should be working OK, and by default, with periodicity (to find
the minimum imaged distance).
On output, radial dumps a summary...
PTRAJ RADIAL: dumping radial distribution functions
50 visits, 446501 measurements from r = 1.637 to 12.000; max r = 12.000
Density is 0.03346 (based on volume is 0.09358). Cell volume is 391726.66289
Are "r" values showing up at short distances like 0.13 or 0.2 A?
I would try seeing if there are differences if you disable imaging (add
"noimage") which would suggest a problem with box size.
An alternative is to use the checkoverlap command to search for short
contacts (shown below for looking at water around residues 1-100)....
checkoverlap :WAT min 0.0 around :1-100
This will show where the short distances are. --tec3
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Received on Fri Sep 16 2011 - 06:30:04 PDT
