[gmx-users] seeming paradox with gmx wham

Alex nedomacho at gmail.com
Mon Mar 12 20:28:32 CET 2018


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.



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

More information about the gromacs.org_gmx-users mailing list