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varsha Offline OP
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I have performed simulation for protein and ligand (unbound state) in NPT ensemble. I want to find their preferential binding coefficient using Kirkwood-Buff (G factor).
After searching in forum, I found a sample script ~/test/c27test/solanal2.inp in which the key RDSP is given for radius. Can anyone tell me how the radius is assigned here?

Thanks in advance.
Varsha

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RDSP is the maximum distance out to which the distance dependent Kirkwood factor is computed. The user chooses RDSP. See corman.doc, and try the testcase to see what it does.


Lennart Nilsson
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varsha Offline OP
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Thank you Lennart. I will try it.

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varsha Offline OP
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The distance-dependent G-factor using solanal2.inp script gives the dipole orientation of sel 1 w.r.t sel 2. I want to find the preferential binding of sel 1 with sel2. So I tried rdf calculation. Is the third column gives the Kirkwood Buff integrals?. If not, is there an option to find KBI?

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You don't say how you obtained the rdfs so I am only guessing about the third column: it contains the number of molecules up to that separation distance. You have to compute the KBI from g(r) (the second column).


Lennart Nilsson
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varsha Offline OP
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Thank you Nilsson for your reply. I used the following lines in the script
coor anal sel segid wat .and. type OH2 end -
site sel segid prot end multi -
firstu 31 nunit 2 skip 10 isdist 21 -
mgn 100 dr 0.1 rsph 999.9 rdsp 15 -
xbox 60.0 ybox 60.0 zbox 60.0

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Yes, that's what I thought; the three columns are R,g(R),N(R)
where N is the number of molecules within distance R of the site.


Lennart Nilsson
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varsha Offline OP
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Thank you Nilsson.


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