AMBER: About WHAM

From: Atsutoshi Okabe <okabe.cherry.bio.titech.ac.jp>
Date: Tue, 21 Feb 2006 15:22:01 +0900

Dear all.

I'm trying to compute potentials of mean force (for distance) using umbrella
sampling with WHAM programs prepared by Dr.Alan Grossfield.

 

Then,I got freefile(outfile) like this:

 

#Coor Free +/- Prob +/-

5.098039 0.237813 nan 0.018599 nan

5.294118 0.272344 nan 0.017543 nan

5.490196 0.208319 nan 0.019551 nan

5.686275 0.179044 nan 0.020544 nan

 

Does Free values(second field) mean A(x) value, A(x)= -kTlnP'(x)-U'(x)+F?

I checked wham.c file of wham programs. So I understood that Free values
corresponds "free_ene[i]".

But I couldn't understand how "free_ene[i]" is computed" in wham programs.

 

Could you please give me a suggestion?

 

A.Okabe



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Received on Sun Feb 26 2006 - 06:10:10 PST
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