How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0?<br><br><div class="gmail_quote">On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;</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 8:18 AM, Nitin Agrawal wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
When I am using the command -zprof0. it is not giving the desired result. I am<br>
using it as<br>
<br>
  g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if 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 and not set to 0.0<br>
<br>
Am i using the parameters wrong?<br>
<br>
</blockquote>
<br></div>
>From g_wham -h:<br>
<br>
&quot;-zprof0      real   0       Define profile to 0.0 at this position (with -log)&quot;<br>
<br>
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.<br>


<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal &lt;<a href="mailto:nitinyugalagrawal@gmail.com" target="_blank">nitinyugalagrawal@gmail.com</a><br></div><div class="im">
&lt;mailto:<a href="mailto:nitinyugalagrawal@gmail.com" target="_blank">nitinyugalagrawal@<u></u>gmail.com</a>&gt;&gt; wrote:<br>
<br>
    Thank you<br>
<br>
<br>
    On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
    &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; 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 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>
        --<br></div>
        ==============================<u></u>__==========<div class="im"><br>
<br>
        Justin A. Lemkul, Ph.D.<br>
        Research Scientist<br>
        Department of Biochemistry<br>
        Virginia Tech<br>
        Blacksburg, VA<br></div>
        jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540) 231-9080<br>
        <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__<a href="http://vt.edu/Pages/Personal/justin" target="_blank"><u></u>vt.edu/Pages/Personal/justin</a><br>
        &lt;<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>&gt;<br>
<br>
        ==============================<u></u>__==========<br>
        --<br>
        gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>
        <a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__<u></u>mailman/listinfo/gmx-users</a><div class="im"><br>
        &lt;<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a>&gt;<br>
        Please search the archive at<br></div>
        <a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists/Search</a><div class="im"><br>
        &lt;<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a>&gt; before posting!<br>
        Please don&#39;t post (un)subscribe requests to the list. Use the www<br>
        interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>&gt;.<br>
        Can&#39;t post? Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists</a><div><div class="h5"><br>
        &lt;<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a>&gt;<br>
<br>
<br>
<br>
<br>
    --<br>
    Regards,<br>
    Nitin Agrawal,<br>
    Master&#39;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>
<br>
<br>
<br>
<br>
--<br>
Regards,<br>
Nitin Agrawal,<br>
Master&#39;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">
<br>
-- <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>
<br>
==============================<u></u>==========<br>
-- <br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don&#39;t post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards,<br>Nitin Agrawal,<br>Master&#39;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>