[gmx-users] Regarding g_wham options
Justin A. Lemkul
jalemkul at vt.edu
Wed May 30 15:20:58 CEST 2012
On 5/30/12 9:17 AM, Nitin Agrawal wrote:
> I got this by using the command :
>
> g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o
> profile_new1.xvg -hist histo_new1.xvg -unit kCal
>
> is their any way to shift the 0 in the y axis so it corresponds to -2 in the
> x-axis. It is just to make the graph look neater and the calculations to become
> easier
>
That's precisely what your command is doing.
The data in the PMF curve are dependent upon how the umbrella sampling
calculations were conducted. There is no way to manipulate the positions of
values along the curve, nor should you want to. The -zprof0 option simply
allows you to choose a convenient reference point, since free energy is
calculated as the difference between two states. Any further manipulation would
be spurious.
-Justin
>
> On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto:nitinyugalagrawal@ <mailto:nitinyugalagrawal@>__gm__ail.com
> <http://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>>
> <mailto: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>
> <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.______vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
> <http://vt.edu/Pages/Personal/__justin
> <http://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/
> <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/
> <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> <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/>
>
>
> --
> ==============================__==========
>
> 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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