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 <[email protected]
<mailto:[email protected]>> 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
========================================
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