[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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