[gmx-users] gmx wham

Justin Lemkul jalemkul at vt.edu
Fri Mar 23 20:10:47 CET 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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