AMBER Archive (2005)

Subject: Re: AMBER: About WHAM program

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Nov 02 2005 - 07:47:01 CST

Hi,

You don't need to manipulate DUMPAVE except perhaps discarding sampling
that's not equilibrated.

hist_min and hist_max define the range of the distance in which the
potential of mean force is calculated. loc_win_min is the center of your
umbrella window, i.e. the value you used for r2 and r3.

Regards,

Guanglei

Atsutoshi Okabe wrote:
> 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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