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
========================================
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