[gmx-users] gmx wham

[Justin Lemkul]

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

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

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