[gmx-users] Problems wtih g_wham

[Jennifer Casey]

Thank you so much!  I appreciate the help, and the good news is actually
great news.

Jenny

On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub <jochen at xray.bmc.uu.se> 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.
>>
>
> Hi Jennifer,
>
> the error message is indeed wrong and should have been "Found ir.ePull =
> constaint" (epullg_names should have been epull_names, one "g" too much in
> gmx_wham.c). I have submitted a bugzilla for that. But the problem was, that
> you did not do umbrella sampling. For umbrella sampling, you restrain the
> system with a (normally harmonic) restraint along the reaction coordinate,
> using "pull = umbrella". You have constrained the system at a fixed position
> along the reaction coordinate, which is not umbrella sampling. However, now
> comes the good news, you can still compute the PMF via the mean forces.
> Average the forces in pullf (after some equilibration), and integrate the
> mean forces (e.g. with g_analyze), giving the potential of mean force (PMF).
> That technique is called something like constrained something calculation or
> so, don't remember exactly.
>
> If you still want to do umbrella sampling, you'll have to do the simulation
> again with pull = umbrella and then use g_wham to get the PMF.
>
> Best wishes,
>
> Jochen
>
>
>
>
>
>
>> I have attached my original pull  .mdp file, and the .mdp file used in the
>> 14 equilibration runs.
>>
>> I appreciate any help.
>>
>> Thanks,
>> Jenny
>>
>
>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Molecular Biophysics group
> Dept. of Cell & Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4714451 Fax: +46-18-511755
> ---------------------------------------------------
>
>
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