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 <jalem...@vt.edu
<mailto:jalem...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<nitinyugalagra...@gmail.com <mailto:nitinyugalagra...@gmail.com>
<mailto:nitinyugalagrawal@__gmail.com
<mailto:nitinyugalagra...@gmail.com>>
<mailto:nitinyugalagrawal@ <mailto:nitinyugalagrawal@>__gm__ail.com
<http://gmail.com>
<mailto:nitinyugalagrawal@__gmail.com
<mailto:nitinyugalagra...@gmail.com>>>> wrote:
Thank you
On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@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.
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Virginia Tech
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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/>>
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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/>>
--
==============================____==========
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>
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University of Turku,Finland
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National Institute of Technology,Durgapur,India
Blog:http://__notjustanyotherblog.blogspot.__com/
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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National Institute of Technology,Durgapur,India
Blog:http://notjustanyotherblog.blogspot.com/
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========================================
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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