Thanks for your reply.<br><br> In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. <br>
<br>Thanks <br>-Aswathy<br><br><div class="gmail_quote">On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
If you defined the reference (r_57) as part of your channel then with pull_geometry=distance you will have problems as the distance between pull_group1 and pull_group0 becomes closer to zero and then the distance becomes positive again.<br>
<br>
I recently had this with my umbrella sampling simulations. Search for the discussion of things you can do to address this issue on the list. To stop this being a problem in the first place you should have used pull_geometry=position.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
Aswathy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Can any one help me please? I looking forward to hear from any of you.<br>
Thank you.<br>
<br>
<br></div><div><div></div><div class="h5">
On Thu, May 6, 2010 at 1:19 PM, Aswathy <<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a> <mailto:<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a>>> wrote:<br>
<br>
Ok i will explain you in detail.<br>
<br>
Initially i pulled the ligand through the protein channel , using<br>
the given parameters.<br>
<br>
pull = umbrella<br>
pull_geometry = distance<br>
pull_dim = N N Y<br>
pull_start = yes<br>
pull_nstxout = 10<br>
pull_nstfout = 10<br>
pull_ngroups = 1<br>
pull_group0 = r_57<br>
pull_group1 = r_C1<br>
pull_rate1 = 0.01<br>
pull_k1 = 1500<br>
<br>
Then I extracted the frames from the trajectory using the perl<br>
program provided with tutorial. COM distance I took as nearly 0.12<br>
nm. (But sometimes I failed to obtain frames exactly at that<br>
interval, but took nearly at 0.12). Each frame I used for Umbrella<br>
sampling for 1ns.<br>
Then I checked histograms for overlapping (Some histograms were<br>
entirely overlapped and I removed that from the list, where ever<br>
gaps i selected new frames and did sampling so that I can get an<br>
evenly distributed histograms , I know this will change the overall<br>
COM distribution but is there any other way to solve this?) .<br>
<br>
Finally once I obtained reasonably good overlapped histograms, I<br>
plotted PMF using g_wham. The plot was a steeply increasing<br>
potential. How can we get increased PMF even when the ligand is<br>
reached out of the channel?<br>
<br>
<br>
<br>
Did I made any mistake any where , I am confused.<br>
<br>
Thank you.<br>
-Aswathy<br>
<br>
<br>
<br>
On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a>>> wrote:<br>
<br>
Aswathy wrote:<br>
<br>
<br>
Hi gromacs users,<br>
<br>
I am using Gromacs 4.0.4 package. I am doing SMD of a ligand<br>
transport through a channel.<br>
<br>
I performed SMD and did umbrella sampling (Thanks to Justin<br>
for his tutorial). Extracted frames with a window spacing<br>
interval of ~0.12nm. and did 1ns sampling. Histograms are<br>
with reasonabvle overlap. Then I used g_wham for plotting<br>
PMF considering first 300ps as equilibration.<br>
<br>
Isn't SMD usually referred to pulling at some finite pulling<br>
speed? That would not be umbrella sampling.<br>
<br>
Anyway, you'll have to provide a lot more data to enable us to<br>
help you.<br>
<br>
Jochen<br>
<br>
<br>
<br>
<br>
I am getting a plot , but potential is increasing<br>
constantly. ie, PMF is not converged as mentioned the<br>
tutorial? Do I need to extend the sampling ? or any other<br>
reason?<br>
<br>
Please help me.<br>
Thank you.<br>
<br>
-Aswathy<br>
<br>
<br>
<br>
-- ---------------------------------------------------<br>
Dr. Jochen Hub<br>
Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4714451 Fax: +46-18-511755<br>
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<br>
<br>
<br>
<br>
-- Aswathy<br>
<br>
<br>
<br>
<br>
-- <br>
Aswathy<br>
<br>
</div></blockquote><font color="#888888">
<br>
-- <br>
Dr Thomas Piggot<br>
University of Southampton, UK.</font><div><div></div><div class="h5"><br>
-- <br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>