[gmx-users] gmx wham

[Justin Lemkul]

On 3/23/18 2:23 PM, Alex wrote:
> Which part is unclear? The image is here: 
> https://www.dropbox.com/s/eiz1m4b69rr3791/pmf_graphene.jpg?dl=0
>
> "below" and "above" correspond to two sets of ion configs below (-1.5 
> nm to 0) and above (0 to 1.5 nm) membrane, respectively. Each curve 
> was pinned with -zprof0 1.5. The reason I did not look at the whole 
> thing is that I probably got confused by the documentation regarding 
> -symm, which suggested relying on PBC when calculating the curve. In 
> my case, nothing crosses periodic boundary. The box is ~ 4 nm tall and 
> configurations are from z=-1.5nm to z=1.5nm. As you can see, there 
> seems to be some sort of a shift going on close to the pore (which is 
> at zero)... In any case, the curve above is consistent with my 
> expectations, while the one below is not.
>

I would expect the -sym option to be relevant, because the profile, as 
you say, should be the same on both sides. However, if you've run the 
simulations such that z is always a positive number, this won't work.

How long are the simulations in each window? Have you done bootstrapping 
for error estimates? The PMF looks a bit rough so I suspect you may not 
have enough data, but indeed the values are strikingly different.

-Justin

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

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