[gmx-users] gmx wham (again)
jhub at gwdg.de
Mon Apr 23 17:18:38 CEST 2018
Hi Alex, hi Justin,
Am 18.04.18 um 09:17 schrieb Alex:
> I suppose this question is mostly for Justin...
> Let me remind what I am dealing with and ask if my idea is correct.
> I have a rectangular membrane in XY with a pore at (X/2, Y/2) in water
> and want to get the Gibbs free energy curve for an ion. For this, I have
> a bunch of starting configurations at (X/2, Y/2) and Z varying between
> some -z0 and z0. The bias in the "fake" pull mdp is applied as N N Y.
> Near the membrane, this means the entire plane is sampled, which adds
> contributions I am not interested in. I want the pore and a small region
> of the membrane around it, not the membrane, given its propertie
> So, I applied weak (k=50) in-plane restraint to the ion for each of the
> sampled configurations -- to keep the sampling region a bit closer to
> the pore. The results look completely different, but they finally make
> very good qualitative sense. The ion still walks around within a small
> disk, but not much -- this tentatively makes me happy.
What you want is a /cylindrical flat-bottomed (FB) position restraint/
around the pore, see the manual for "flat-bottomed position restraints".
You will make sure that the ion stays close the pore in the xy-plane,
and this way you avoid sampling problems at the pore entry and exit.
Note that the FB position restraint will change the entropy of the ion
in the x-y plane. The entropic correction needed for your PMFs (to
remove the contribution form the flat-bottomed restraint) is worked out
in Appendix of this paper:
This correction allows you to refer your PMF to a well-defined /area per
pore/ or, equivalently, /density of pores/ in the membrane (which
sometimes causes a lot of confusion).
I would definitely not use a simple (not flat-bottomed) position
restraint to restrain the ion near the pore - this may cause artifacts
in your PMF.
The cylinder-based reaction coordinate (mentioned by Justin) affects how
the center of mass of the membrane is computed in Z-direction. Hence, it
changes the *reaction coordinate*. But it does *not* affect the sampled
xy-plane of the ion.
The idea behind the cylinder-based reaction coordinate is to avoid that
permeation barriers are smeared out due to membrane undulations. Hence,
for a small membrane that hardly undulates, a simple reaction coordinate
is probably fine (using pull_coord1_geometry = direction or
I hope this helped.
> Would you believe the results obtained this way, assuming otherwise
> proper setup?
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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