AMBER Archive (2005)

Subject: AMBER: About WHAM program

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Tue Nov 01 2005 - 21:29:14 CST

Dear all

I want to calculate potentials of mean force(for distance,2$B"r!A#2#0"r(B 0.1$B"r(B
/bin) using umbrella sampling in Amber8.

So I could get a DUMPAVE file.(The first field is each time point, the
second field is

the values of the reaction coordinate)

But I can't understand how to manipulate the DUMPAVE file in WHAM program.

I read the WHAM manual written by Pro. Alan Grossfield , but I can't
understand.

I can't also understand "wham" command. What does "hist_min and hist_max"
mean

in my case ? Doest it mean that "hist_min = 2, hist_max = 20" ?

Adittionally I can't understand metadatafile formats. What does
"loc_win_min"

mean in my case ?

Could you please give me a suggestion?

Thank you

Atsutoshi Okabe

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