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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