# [gmx-users] Regarding g_wham options

Justin A. Lemkul jalemkul at vt.edu
Wed May 30 15:08:30 CEST 2012

```
On 5/30/12 8:57 AM, Nitin Agrawal wrote:
> How can I define the value at y axis then? Is there any way to bring the y-axis
> value down to 0?
>

You want the energy minimum to be equal to zero, correct?  This is nothing more
than a reference point, so the value passed to -zprof0 is the coordinate value
(x-axis) at which the energy minimum occurs.  Setting a proper value will shift
the curve such that the energy minimum is at zero.

-Justin

> On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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>
>         <mailto: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>
>         <mailto: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> <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>         <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/
>         <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/
>         <http://notjustanyotherblog.blogspot.com/>
>
>
>     --
>     ==============================__==========
>
>     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/

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

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

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

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