[gmx-users] Problems wtih g_wham

Jennifer Casey jrcasey20 at gmail.com
Sat Feb 13 18:08:57 CET 2010

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.


On Fri, Feb 12, 2010 at 6:12 PM, Justin A. Lemkul <jalemkul at 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
> 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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