[gmx-users] Problems wtih g_wham

[Justin A. Lemkul]

Jennifer Casey wrote:
> 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. 
> 

Right, that's why I provide .mdp files for each step that should be, in general, 
usable (with a few tweaks dependent upon the system).  I'll think about making 
the tutorial a bit more explicit.

> 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. 
> 

I don't see how the code could have told you that you were using cylinder, which 
is a "pull_geometry" option, not a "pull" option (see .mdp parameters in the 
manual).  If it did, then there could be a bug in the code, but from looking at 
where the error originates in gmx_wham.c, it seems to be calling the right enum, 
so I don't know how it would've printed "cylinder."

-Justin

> Thanks,
> Jenny
> 
> On Fri, Feb 12, 2010 at 6:12 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
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> 

-- 
========================================

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

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