Dear Amber user,
I came across this advice on the amber mailing list concerning the use of
xmgrace to determine number of water molecules from a point:
"It sounds to me like the analysis you want to do is to calculate a radial
distribution function in ptraj (which will effectively give you a graph of
how many solvent molecules are present as a function of distance from a
given solute mask). This is described in the manual via the "radial"
command.
If you integrate the RDF from 0 to whichever distance you want, that should
give you the number of water molecules within that distance cutoff of the
Zn ion (something that xmgrace does very easily under
Data->Transformations->Integration)".
My question is asked to clarify on the point made in the advice. From my
understanding, the value given after following: Data -> Transformations ->
Integration is the total number of water molecules (i.e. the area under the
entire curve from 0 to the last point on the x-axis). Am i correct in
assuming that? I have performed a test where i have a smaller value on the
x-axis as the end point and it seems to agree with this assumption. Am only
asking so as to make sure that my assumption is not wrong.
Thank you
Syl
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Received on Fri May 22 2015 - 13:00:04 PDT
