[gmx-users] gmx wham (again)

[Justin Lemkul]

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

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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