[gmx-users] seeming paradox with gmx wham

[Alex]

Sorry, i meant 4 nm tall, not wide.


On 3/12/2018 1:42 PM, Alex wrote:
> 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?
>
> Thanks,
>
> Alex
>
>
> 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
>>>>
>>>
>>
>