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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