[gmx-users] Problems wtih g_wham
jrcasey20 at gmail.com
Sat Feb 13 18:08:57 CET 2010
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:
>> 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.
> 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
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