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.H* :THF.O2 closest density 0.033456
radial rdf0.00o1thfwater 0.05 10.00 :WAT.H* :THF.O1 closest density 0.033456
radial rdf0.00oe2thfwater 0.05 10.00 :WAT.H* :THF.OE2 closest density
0.033456
radial rdf0.00oe1thfwater 0.05 10.00 :WAT.H* :THF.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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Received on Mon Sep 14 2009 - 13:40:57 PDT
