Thank you so much! I appreciate the help, and the good news is actually great news.
Jenny On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub <joc...@xray.bmc.uu.se> wrote: > Jennifer Casey wrote: > >> Hello, >> >> 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. >> > > Hi Jennifer, > > 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. > > 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. > > Best wishes, > > Jochen > > > > > > >> I have attached my original pull .mdp file, and the .mdp file used in the >> 14 equilibration runs. >> >> I appreciate any help. >> >> Thanks, >> Jenny >> > > > -- > --------------------------------------------------- > Dr. Jochen Hub > Molecular Biophysics group > Dept. of Cell & Molecular Biology > Uppsala University. Box 596, 75124 Uppsala, Sweden. > Phone: +46-18-4714451 Fax: +46-18-511755 > --------------------------------------------------- > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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