[gmx-users] gmx wham

Alex nedomacho at gmail.com
Fri Mar 23 19:23:02 CET 2018

Which part is unclear? The image is here: 

"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'm not sure I follow. Can you provide images of the PMF profiles, or 
> actual numbers and error bars? I'm sort of guessing that you're just 
> getting an asymmetric result in a symmetric system, which can be due 
> to a lot of factors, mostly just sampling. And is there a reason you 
> are not evaluating just one, symmetric PMF profile with gmx wham -symm?
> -Justin

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