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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>
<mailto:nitinyugalagrawal@__gmail.com
<mailto:[email protected]>>> wrote:
Thank you
On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
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==============================____==========
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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/>
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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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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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