[gmx-users] Regarding g_wham options

[Justin A. Lemkul]

On 5/30/12 8:18 AM, Nitin Agrawal wrote:
> When I am using the command -zprof0. it is not giving the desired result. I am
> using it as
>
>   g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if pullf_files.dat -o
> profile_new1.xvg -hist histo_new1.xvg -unit kCal
>
> but the lowest point in the graph is still -6.0 in the y axis and not set to 0.0
>
> Am i using the parameters wrong?
>

 From g_wham -h:

"-zprof0      real   0       Define profile to 0.0 at this position (with -log)"

The value provided should be the point along the x-axis (the reaction 
coordinate) where you want the value of the PMF (on the y-axis) to be zero. 
Your original plot only contained values between about -2 and 2, so specifying 
-6 is not valid.

-Justin

> On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal <nitinyugalagrawal at gmail.com
> <mailto:nitinyugalagrawal at gmail.com>> wrote:
>
>     Thank you
>
>
>     On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>         On 5/30/12 6:29 AM, Nitin Agrawal wrote:
>
>             Hi all,
>
>             I want to set the lowest point in my curve as zero instead of
>             negative number.
>             Can anyone tell me which option to use to do that?
>
>
>         Set the desired value with -zprof0.
>
>         -Justin
>
>         --
>         ==============================__==========
>
>         Justin A. Lemkul, Ph.D.
>         Research Scientist
>         Department of Biochemistry
>         Virginia Tech
>         Blacksburg, VA
>         jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>         ==============================__==========
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>     --
>     Regards,
>     Nitin Agrawal,
>     Master's Student (Bioinformatics)
>     University of Turku,Finland
>     B.Tech (Biotechnology)
>     National Institute of Technology,Durgapur,India
>     Blog:http://notjustanyotherblog.blogspot.com/
>
>
>
>
> --
> Regards,
> Nitin Agrawal,
> Master's Student (Bioinformatics)
> University of Turku,Finland
> B.Tech (Biotechnology)
> National Institute of Technology,Durgapur,India
> Blog:http://notjustanyotherblog.blogspot.com/

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================