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'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"><<a href="mailto:jalemkul@vt.edu">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>
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'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 <<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>
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? >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'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>
<<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></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>
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'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>
<<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a> <mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>><br>
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<mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><u></u>>__>__>> 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>
<<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>
<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>>><br>
<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>><br>
<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>
rajat desikan wrote:<br>
<br>
Hi<br>
I am a new gromacs user. I just completed Justin'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>
-- ==============================<u></u>______==========<div class="im"><br>
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Justin A. Lemkul<br>
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-- <br>
Rajat Desikan (Ph.D Scholar)<br>
Prof. K. Ganapathy Ayappa'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>
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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's Lab (no 13),<br>Dept. of Chemical Engineering,<br>Indian Institute of Science, Bangalore<br>
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