[AMBER] Determining number of molecules from a point by integration using xmgrace

From: Sylvester Tumusiime <stumusii.uno.edu>
Date: Fri, 22 May 2015 19:48:26 +0000

   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"


   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


   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

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Received on Fri May 22 2015 - 13:00:04 PDT
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