[gmx-users] Problems wtih g_wham

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 13 03:12:24 CET 2010

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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