Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it&#39;s position, sort of going back and forth.<div>
Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations?<br>
<div><div><br><div class="gmail_quote">On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">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>
rajat desikan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
Should i turn off charges on the methane molecules? I have left them on.<br>
<br>
</blockquote>
<br></div>
What force field are you using?  If you&#39;ve got an all-atom model of methane, you should have partial charges.<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 Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>

<br>
<br>
<br>
    rajat desikan wrote:<br>
<br>
        My simulations are for 10 ns in each window. There is a lot of<br>
        noise in my wham too. I am enclosing my wham for pullf (the<br>
        earlier was pullx) and pmf. They are really looking strange.<br>
        Stronger restraint means force constant? &gt;From literature, I<br>
        kept it at 3000.<br>
<br>
<br>
    Those plots do look very strange.  The PMF is almost a step<br>
    function, which is certainly wrong.  You may need either more<br>
    simulation time or more frequent collection of data points, but at<br>
    this stage I can only guess.  Not much more I can offer, sorry.<br>
<br>
    A stronger restraint would mean a stronger force constant, yes, but<br>
    if you&#39;re using 3000 to restrain simple molecules like methane, I<br>
    think there is no need to increase it.<br>
<br>
    -Justin<br>
<br>
        On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div><div class="im">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
           rajat desikan wrote:<br>
<br></div><div><div class="h5">
               hi Justin<br>
               I am not able to tell where the lack of overlap is. This<br>
        is the<br>
               first wham plot I am looking at. In your tutorial and<br>
               literature, the wham plots are so clear. Can you please<br>
        help me?<br>
               Thanks.<br>
<br>
<br>
           It looks like your first one or two windows were not restrained<br>
           sufficiently at the desired distance.  The error complains<br>
        that bin<br>
           2 should have points at 0.366 nm, but it appears neither bin<br>
        1 nor<br>
           bin 2 satisfy this requirement. Check carefully what you have set<br>
           for reference distances and what distances were actually<br>
        maintained<br>
           during the sampling.  You may need a stronger restraint or longer<br>
           simulations.  How long are the simulations?  I see that you&#39;re<br>
           starting the analysis on data after 2 ns, but how much does<br>
        that leave?<br>
<br>
           -Justin<br>
<br>
               On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan<br>
               &lt;<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a> &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>&gt;<br>
        &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a> &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>&gt;__&gt;<br>
               &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><br>
        &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>&gt;<br>
<br>
               &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><br></div></div><div><div class="h5">
        &lt;mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>&gt;__&gt;__&gt;&gt; wrote:<br>
<br>
                  Oh lovely...thanks for the quick reply Justin :)...<br>
<br>
<br>
                  On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul<br>
               &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
                  &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
                      rajat desikan wrote:<br>
<br>
                          Hi<br>
                          I am a new gromacs user. I just completed Justin&#39;s<br>
               umbrella<br>
                          sampling tutorial. I am doing a PMF<br>
        calculation between 2<br>
                          methane molecules in water. The simulation has run<br>
               fine till<br>
                          the g_wham step. My command is<br>
<br>
                          -- g_wham -it tpr-files.dat -if<br>
        pullf-files.dat -o -hist<br>
                          -unit kCal -b 2000<br>
<br>
                          I get a warning:<br>
                          WARNING, no data point in bin 2 (z=0.366256) !<br>
                          You may not get a reasonable profile. Check your<br>
               histograms!<br>
<br>
                          and my histogram contains a single peak.<br>
<br>
                          I have pulled my other methane 1 nm away from<br>
        the first<br>
                          methane. I have 15 sampling windows (0.05 nm apart<br>
               till 5nm<br>
                          and then 1 nm apart)...can you please tell me<br>
        how to<br>
               correct<br>
                          this?<br>
<br>
<br>
                      With 15 windows, you should have 15 histograms.<br>
         Plot with:<br>
<br>
                      xmgrace -nxy histo.xvg<br>
<br>
                      It will show you where the lack of sampling is.<br>
<br>
                      -Justin<br>
<br></div></div>
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                      Justin A. Lemkul<br>
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                      Department of Biochemistry<br>
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           Justin A. Lemkul<br>
           Ph.D. Candidate<br>
           ICTAS Doctoral Scholar<br>
           MILES-IGERT Trainee<br>
           Department of Biochemistry<br>
           Virginia Tech<br>
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        --         Rajat Desikan (Ph.D Scholar)<br>
        Prof. K. Ganapathy Ayappa&#39;s Lab (no 13),<br>
        Dept. of Chemical Engineering,<br>
        Indian Institute of Science, Bangalore<br>
<br></div></div>
        ------------------------------<u></u>__----------------------------<u></u>--__------------<div><div class="h5"><br>
<br>
<br>
        ------------------------------<u></u>__----------------------------<u></u>--__------------<br>
<br>
<br>
    --     ==============================<u></u>__==========<br>
<br>
    Justin A. Lemkul<br>
    Ph.D. Candidate<br>
    ICTAS Doctoral Scholar<br>
    MILES-IGERT Trainee<br>
    Department of Biochemistry<br>
    Virginia Tech<br>
    Blacksburg, VA<br>
    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>
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<br>
<br>
<br>
<br>
-- <br>
Rajat Desikan (Ph.D Scholar)<br>
Prof. K. Ganapathy Ayappa&#39;s Lab (no 13),<br>
Dept. of Chemical Engineering,<br>
Indian Institute of Science, Bangalore<br>
</div></div></blockquote>
<br><div class="HOEnZb"><div class="h5">
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Rajat Desikan (Ph.D Scholar)<br>Prof. K. Ganapathy Ayappa&#39;s Lab (no 13),<br>Dept. of Chemical Engineering,<br>Indian Institute of Science, Bangalore<br>

</div></div></div>