[gmx-users] gmx wham

[Justin Lemkul]

On 3/21/18 7:56 PM, Alex wrote:
> Hi all,
>
> I have a solvated membrane with a pore and I'm basically following Justin's
> tutorial on calculating free energy for an ion. There is a total of 30
> configurations of the ion relative to the membrane, 15 above membrane, 15
> below. The spacing between configurations is reasonable for a single ion,
> at least from what I can see (0.1 nm).
>
> With wham applied to each half, I get different curves, although they are
> perfectly equivalent in terms of configurations and the pore is absolutely
> symmetric height-wise (it's really a graphene membrane with a hole).
> Not different in the sense they're shifted, but after both curves are
> properly shifted to make "bulk" region correspond to zero deltaG.
>
> Any ideas?

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

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