[gmx-users] seeming paradox with gmx wham

Justin Lemkul jalemkul at vt.edu
Mon Mar 12 20:35:19 CET 2018

On 3/12/18 3:28 PM, Alex wrote:
> Thanks!
> Just to make sure I'm doing this right this time. By merely changing 
> the dim directive with everything else following your tutorial, I 
> would be probing the spherical domain around the pore with a bunch of 
> different radius values? Because this is exactly what I want.

Yes, you're applying a 1-D bias when you actually want a 3-D bias. 
People often misuse the tutorial .mdp files, though I will have a new 
version of the tutorial out this summer (along with a paper) that should 
clear all this up.


> Thanks,
> Alex
> On 3/12/2018 8:43 AM, Justin Lemkul wrote:
>> 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


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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