[gmx-users] gmx wham (again)

Justin Lemkul jalemkul at vt.edu
Wed Apr 18 15:08:37 CEST 2018

On 4/18/18 3:17 AM, Alex wrote:
> 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 
> properties.
> 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.
> Would you believe the results obtained this way, assuming otherwise 
> proper setup?

This is the exact situation that the "cylinder" pull geometry is 
designed to model. I suggest going that route rather than ad hoc 
restraints, which will influence the PMF and should be otherwise 
accounted for.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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