[gmx-users] seeming paradox with gmx wham

Alex nedomacho at gmail.com
Mon Mar 12 20:42:36 CET 2018

I actually understood your tutorial perfectly well. What I didn't expect 
is such a significant dependence on direction (assuming spherical 
symmetry clears the situation).

I also had to use direction-periodic instead of distance in your 
tutorial, because the box is 4 nm wide and grompp is screaming about 
distance exceeding half-box size. I used 5.0.3 before and it was fine 
with the 'distance' directive. I think 'direction-periodic' is also 
wrong for spherical symmetry. So, stick with distance and increase box size?



On 3/12/2018 1:35 PM, Justin Lemkul wrote:
> 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.
> -Justin
>> 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

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