Can any one help me please? I looking forward to hear from any of you.<br>Thank you.<br><br><br><div class="gmail_quote">On Thu, May 6, 2010 at 1:19 PM, Aswathy <span dir="ltr"><<a href="mailto:ammasachu@gmail.com">ammasachu@gmail.com</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;">Ok i will explain you in detail.<br><br> Initially i pulled the ligand through the protein channel , using 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 program provided with tutorial. COM distance I took as nearly 0.12 nm. (But sometimes I failed to obtain frames exactly at that interval, but took nearly at 0.12). Each frame I used for Umbrella sampling for 1ns. <br>
Then I checked histograms for overlapping (Some histograms were entirely overlapped and I removed that from the list, where ever gaps i selected new frames and did sampling so that I can get an evenly distributed histograms , I know this will change the overall COM distribution but is there any other way to solve this?) . <br>
<br>Finally once I obtained reasonably good overlapped histograms, I plotted PMF using g_wham. The plot was a steeply increasing potential. How can we get increased PMF even when the ligand is reached out of the channel? <br>
</blockquote><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Did I made any mistake any where , I am confused.<br>
<br>Thank you.<br>-Aswathy<div><div></div><div class="h5"><br><br><br><div class="gmail_quote">On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</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;">
<div>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;">
<br>
Hi gromacs users,<br>
<br>
I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel.<br>
<br>
I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasonabvle overlap. Then I used g_wham for plotting PMF considering first 300ps as equilibration.<br>
</blockquote></div>
Isn't SMD usually referred to pulling at some finite pulling speed? That would not be umbrella sampling.<br>
<br>
Anyway, you'll have to provide a lot more data to enable us to help you.<br>
<br>
Jochen<div><br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason?<br>
<br>
Please help me.<br>
Thank you.<br>
<br>
-Aswathy<br>
</blockquote>
<br>
<br></div>
-- <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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</font></blockquote></div><br><br clear="all"><br></div></div>-- <br><font color="#888888">Aswathy<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>