[gmx-users] seeming paradox with gmx wham
jalemkul at vt.edu
Mon Mar 12 20:35:19 CET 2018
On 3/12/18 3:28 PM, Alex wrote:
> 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.
> 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
>> 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.
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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