Justin,<div>Should i turn off charges on the methane molecules? I have left them on.<br><br><div class="gmail_quote">On Mon, Nov 21, 2011 at 12:32 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">
My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? >From literature, I kept it at 3000.<br>
<br>
</blockquote>
<br></div>
Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at 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 if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it.<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 Sun, Nov 20, 2011 at 9:12 PM, 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></div><div class="im">
hi Justin<br>
I am not able to tell where the lack of overlap is. This 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 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 that bin<br>
2 should have points at 0.366 nm, but it appears neither bin 1 nor<br>
bin 2 satisfy this requirement. Check carefully what you have set<br>
for reference distances and what distances were actually 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 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></div>
<mailto:<a href="mailto:rajatdesikan@gmail.com" target="_blank">rajatdesikan@gmail.com</a><div class="im"><br>
<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></div><div><div class="h5">
<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 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 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 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 how to<br>
correct<br>
this?<br>
<br>
<br>
With 15 windows, you should have 15 histograms. 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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------------------------------<u></u>__----------------------------<u></u>--__------------<div><div class="h5"><br>
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------------------------------<u></u>------------------------------<u></u>------------<br>
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------------------------------<u></u>------------------------------<u></u>------------<br>
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</blockquote><div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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