Thank you so much! I appreciate the help, and the good news is actually great news.<br><br>Jenny<br><br><div class="gmail_quote">On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">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 class="im">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>
</blockquote>
<br></div>
Hi Jennifer,<br>
<br>
the error message is indeed wrong and should have been "Found ir.ePull = constaint" (epullg_names should have been epull_names, one "g" too much in gmx_wham.c). I have submitted a bugzilla for that. But the problem was, that you did not do umbrella sampling. For umbrella sampling, you restrain the system with a (normally harmonic) restraint along the reaction coordinate, using "pull = umbrella". You have constrained the system at a fixed position along the reaction coordinate, which is not umbrella sampling. However, now comes the good news, you can still compute the PMF via the mean forces. Average the forces in pullf (after some equilibration), and integrate the mean forces (e.g. with g_analyze), giving the potential of mean force (PMF). That technique is called something like constrained something calculation or so, don't remember exactly.<br>
<br>
If you still want to do umbrella sampling, you'll have to do the simulation again with pull = umbrella and then use g_wham to get the PMF.<br>
<br>
Best wishes,<br>
<br>
Jochen<div class="im"><br>
<br>
<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 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>
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<br></div><font color="#888888">
-- <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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