Hello again, 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"
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. 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. Thanks, Jenny On Fri, Feb 12, 2010 at 6:12 PM, Justin A. Lemkul <jalem...@vt.edu> 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. >> >> > 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. > > -Justin > > > I have attached my original pull .mdp file, and the .mdp file used in the >> 14 equilibration runs. >> >> I appreciate any help. >> >> Thanks, >> Jenny >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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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