[gmx-users] seeming paradox with gmx wham

[Justin Lemkul]

On 3/11/18 8:05 PM, Alex wrote:
> Just to add to my question... The pull code for the umbrella sampling 
> from each of the N configs, as used in Justin's tutorial, is
>
> pull_coord1_type        = umbrella
> pull_coord1_geometry    = distance
> ...
> pull_coord1_dim         = N N Y
>
> So, in each of the generated pullf and pullx files we sample a flat 
> slice at a given Z, and the reported forces and displacements are 
> along Z. What appears to be the reaction coordinate in our case is the 
> radius from the pore mouth, and one has to sample a set of hemispheres 
> from a series of radius values. Is this at all a possibility?
>

Yes, but not by following the tutorial. You'd need to use 
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around 
the pore itself. As it is, you're probably underestimating entropic 
contributions to the free energy.

-Justin

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

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