AMBER Archive (2009)

Subject: [AMBER] question with radial distribution function

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Thu Sep 10 2009 - 17:08:34 CDT

Hi all,

I am trying to compute the pairwise rdf for the O on the substrate and
nearby water inside the pore of the enzyme
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.

Also is there a way to compute the number integrals from these rdfs.

thanks for your time and help.

regards,

ganesh
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