AMBER Archive (2006)

Subject: AMBER: About WHAM

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Tue Feb 21 2006 - 00:22:01 CST

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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