AMBER Archive (2009)

Subject: [AMBER] radial distribution function in amber

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Mon Sep 14 2009 - 09:58:56 CDT


Hi all,

I am trying to compute the pairwise rdf for the O and nearby water using the
these commands.

trajin data-0.00.crd
image origin center
radial rdf0.00o2thfwater 0.05 10.00 :WAT_at_H* :THF_at_O2 closest density 0.033456
radial rdf0.00o1thfwater 0.05 10.00 :WAT_at_H* :THF_at_O1 closest density 0.033456
radial rdf0.00oe2thfwater 0.05 10.00 :WAT_at_H* :THF_at_OE2 closest density
0.033456
radial rdf0.00oe1thfwater 0.05 10.00 :WAT_at_H* :THF_at_OE1 closest density
0.033456
go

However when I look at the carnal or standard.xmgr i see that rdf doesnot
converge to a value of 1.
Could you help me how I could rectify this. Do I need to specify a volume or
change the density number.

thanks,

ganesh
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