Ok, Thank you once again.<br><br><div class="gmail_quote">On Wed, May 30, 2012 at 4:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 5/30/12 9:17 AM, Nitin Agrawal wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I got this by using the command :<br>
<br>
g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o<br>
profile_new1.xvg -hist histo_new1.xvg -unit kCal<br>
<br>
is their any way to shift the 0 in the y axis so it corresponds to -2 in the<br>
x-axis. It is just to make the graph look neater and the calculations to become<br>
easier<br>
<br>
</blockquote>
<br></div>
That's precisely what your command is doing.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><div class="im">
On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
On 5/30/12 8:57 AM, Nitin Agrawal wrote:<br>
<br>
How can I define the value at y axis then? Is there any way to bring the<br>
y-axis<br>
value down to 0?<br>
<br>
<br>
You want the energy minimum to be equal to zero, correct? This is nothing<br>
more than a reference point, so the value passed to -zprof0 is the<br>
coordinate value (x-axis) at which the energy minimum occurs. Setting a<br>
proper value will shift the curve such that the energy minimum is at zero.<br>
<br>
-Justin<br>
<br>
On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br></div><div class="im">
On 5/30/12 8:18 AM, Nitin Agrawal wrote:<br>
<br>
When I am using the command -zprof0. it is not giving the desired<br>
result. I am<br>
using it as<br>
<br>
g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if<br>
pullf_files.dat -o<br>
profile_new1.xvg -hist histo_new1.xvg -unit kCal<br>
<br>
but the lowest point in the graph is still -6.0 in the y axis<br>
and not<br>
set to 0.0<br>
<br>
Am i using the parameters wrong?<br>
<br>
<br>
>From g_wham -h:<br>
<br>
"-zprof0 real 0 Define profile to 0.0 at this position<br>
(with -log)"<br>
<br>
The value provided should be the point along the x-axis (the reaction<br>
coordinate) where you want the value of the PMF (on the y-axis) to<br>
be zero.<br>
Your original plot only contained values between about -2 and 2, so<br>
specifying -6 is not valid.<br>
<br>
-Justin<br>
<br>
On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal<br>
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<mailto:<a href="mailto:nitinyugalagrawal@gmail.com" target="_blank">nitinyugalagrawal@<u></u>gmail.com</a>>>>> wrote:<br>
<br>
Thank you<br>
<br>
<br>
On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
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<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> wrote:<br>
<br>
<br>
<br>
On 5/30/12 6:29 AM, Nitin Agrawal wrote:<br>
<br>
Hi all,<br>
<br>
I want to set the lowest point in my curve as zero<br>
instead of<br>
negative number.<br>
Can anyone tell me which option to use to do that?<br>
<br>
<br>
Set the desired value with -zprof0.<br>
<br>
-Justin<br>
<br>
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==============================<u></u>______==========<div class="im"><br>
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Virginia Tech<br>
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==============================<u></u>__==========<br>
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Regards,<br>
Nitin Agrawal,<br>
Master's Student (Bioinformatics)<br>
University of Turku,Finland<br>
B.Tech (Biotechnology)<br>
National Institute of Technology,Durgapur,India<br>
Blog:<a href="http://notjustanyotherblog.blogspot.com/" target="_blank">http://<u></u>notjustanyotherblog.blogspot.<u></u>com/</a><br>
</div></div></blockquote><div class="HOEnZb"><div class="h5">
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-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards,<br>Nitin Agrawal,<br>Master's Student (Bioinformatics)<br>University of Turku,Finland<br>B.Tech (Biotechnology)<br>National Institute of Technology,Durgapur,India<br>
Blog:<a href="http://notjustanyotherblog.blogspot.com/" target="_blank">http://notjustanyotherblog.blogspot.com/</a><br>