Hi,
Sorry for the delay on this. The answer is pretty straightforward
actually - the "raw" RDF is literally that - just the total bin
counts, so if you're doing more than one frame you'll easily get more
than the total number of waters in the system. Try it on a single
frame to see what I mean. Hope this helps,
-Dan
On Thu, Sep 8, 2022 at 4:02 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Hi Dan,
>
> I mean that the number of waters+Na+ is 59559, and the raw RDF quickly exceeds 100,000.
>
> Best,
> Matthew
>
>
>
> > On Sep 8, 2022, at 3:59 PM, Daniel Roe via AMBER <amber.ambermd.org> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > Hi,
> >
> > Unless I misunderstand you, you are selecting both water and sodium, so the
> > count should exceed the number of waters, right?
> >
> > -Dan
> >
> > On Thu, Sep 8, 2022 at 2:55 PM Matthew Guberman-Pfeffer via AMBER <
> > amber.ambermd.org> wrote:
> >
> >> Dear Amber Community,
> >>
> >> The below CPPTRAJ command gives me raw RDF values that exceed the number
> >> of waters in the simulation box:
> >>
> >> radial out rdf.dat 0.1 15 :WAT,Na+ :1280 density 0.033456 intrdf
> >> intrdf.dat rawrdf rawrdf.dat bymol1
> >>
> >> Is it an imaging issue?
> >>
> >> What I’m really concerned about is the same command run on two different
> >> trajectories with identical counts of WAT and Na+ gives me raw RDF values
> >> that almost systematically differ by a factor of ~2. The only difference
> >> between the simulations is the temperature. I need to know if the
> >> difference is real.
> >>
> >> Best,
> >> Matthew
> >>
> >>
> >>
> >>
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Received on Tue Sep 13 2022 - 05:30:03 PDT
