[gmx-users] gmx wham

Justin Lemkul jalemkul at vt.edu
Fri Mar 23 20:27:33 CET 2018

On 3/23/18 3:22 PM, Alex wrote:
> My understanding of the value of Z is that it is the distance between COMs,
> i.e. that would always be positive -- correct me if i'm wrong. The

It depends on how you set things up. The displacement is a vector, so 
you can in principle set things up to have both positive and negative 
values along the reaction coordinate.

> configurations in terms of absolute coordinates are as follows: the
> membrane is at z = 2 nm, the below portion is then 0.5 nm to 2 nm and the
> above portion is 2 nm to 3.5 nm. The box is of course 0 to 4 nm in Z. I
> left all boostrapping options to defaults. The roughness of graphs is on
> one hand no different from those in the paper first describing g_wham, but
> on the other my configurations may be too far apart for the region near the
> pore. I suspect it is critical, because this pore pulls things quite a bit.
> As far as per-config simulations go, i actually things are sufficient with
> 4 ns. I had a set of 10 ns long ones, no difference.
> Denser spacing between configs?

Possibly. I'd check the histograms to see if there are any areas of weak 
sampling that could be skewing things.



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

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