[gmx-users] seeming paradox with gmx wham

Justin Lemkul jalemkul at vt.edu
Mon Mar 12 15:43:28 CET 2018

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 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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