[gmx-users] gmx wham (again)

Alex nedomacho at gmail.com
Wed Apr 18 09:17:07 CEST 2018

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?



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