Oh lovely...thanks for the quick reply Justin :)...<br><br><div class="gmail_quote">On Sat, Nov 19, 2011 at 10:57 PM, 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">
Hi<br>
I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is<br>
<br>
-- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -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 histograms!<br>
<br>
and my histogram contains a single peak.<br>
<br>
I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this?<br>
<br>
</blockquote>
<br></div>
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>
-- <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>==========<span class="HOEnZb"><font color="#888888"><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'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'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>
</font></span></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>