Hello again,<br><br>When I was working through your tutorial, I noticed the following statement under pull = umbrella: "IMPORTANT: This procedure is not umbrella sampling. I used a harmonic potential.....For the purposes of generating initial configurations for umbrella sampling, you can set pull = constraint with equivalent results"<br>
<br>I guess I just focused on the first part. I didn't realize that I needed to switch to pull = umbrella in order to use g_wham. <br><br>I still don't understand the part of the error where pull = cylinder though (I am sure that it said this). I will change pull = constraint to pull = umbrella and see if I still get the error. <br>
<br>Thanks,<br>Jenny <br><br><div class="gmail_quote">On Fri, Feb 12, 2010 at 6:12 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Jennifer Casey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am trying to create a PMF for the sodium cation and iodine anion in the presence of THF. I have been following the umbrella sampling tutorial on the gromacs website, and everything has been working out. I have finally created 14 different equilibriation simulations, whose starting configurations were obtained form a pull simulation with pull_rate = 0.06. To get the 14 different equilibriated runs, I left the pull code on, but I just made pull_rate = 0.00. I have created a list of the .tpr files and the pullf[].xvg files, and I tried to use g_wham. The error I got was as follows: "This is not a tpr of an umbrella simulation. Found ir.ePul; = cylinder." Has anyone else found this error? I was not even using cylinder, I was using distance.<br>
<br>
</blockquote>
<br></div>
Your .mdp files indicate "pull = constraint" so the error message is at least partially correct - you are not using umbrella sampling (that would be "pull = umbrella"). Perhaps this is just a typo and the error did actually say "constraint" but in any case, WHAM won't work unless you're actually doing umbrella sampling.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have attached my original pull .mdp file, and the .mdp file used in the 14 equilibration runs.<br>
<br>
I appreciate any help.<br>
<br>
Thanks,<br>
Jenny <br>
</blockquote>
<br></div>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><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/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>