[gmx-users] GMX 2018 and 'distance' pull

[Alex]

>
> It's the force on the spring connecting the two groups.
>
So, then, it's what I said. In any case, I must say that the probe along 
Z was more representative of the reality: a hemispherical slice probes a 
circle near the surface of the membrane, which has nothing to do with 
the pore, but naturally produces a barrier. I wish there was a way to 
probe a spherical symmetry within a given solid angle. If pullf/pullx 
data had any angular info, we could script our own implementation of 
WHAM, but alas.

Alex

>> code would clarify, because the result of wham now looks rather 
>> strange -- a long (1.5 nm!) hydration barrier for the ion. Makes 
>> little physical sense and very different from the bias along Z case.
>>
>> I am guessing that the sampling of 1 ns per hemispherical slice is 
>> far from sufficient to probe that space... Just looked at one of the 
>> trajectories there -- the ion is nowhere near moving around the 
>> entire slice.
>>
>> Alex
>>
>>
>> On 3/13/2018 10:27 AM, Justin Lemkul wrote:
>>>
>>>
>>> On 3/13/18 10:32 AM, Alex wrote:
>>>> It appears that things have improved... I am just glancing and 
>>>> pullf and pullx data from the first sample config and both contain 
>>>> only one value, even though we set dim to 3D. Does this make sense?
>>>>
>>>
>>> I haven't used the 2018 pull code yet. Presumably this is correct, 
>>> just the distance rather than all its components, though that would 
>>> be a change from previous versions.
>>>
>>> -Justin
>>>
>>>> Thanks,
>>>>
>>>> Alex
>>>>
>>>> On 3/13/2018 8:18 AM, Justin Lemkul wrote:
>>>>>
>>>>>
>>>>> On 3/13/18 10:17 AM, Alex wrote:
>>>>>> Justin,
>>>>>>>> You may have a situation that requires manual assignment of 
>>>>>>>> pull_group1_pbcatom1, as the automatic choice of 
>>>>>>>
>>>>>>> Sorry, that should be pull_group1_pbcatom. Must remind myself 
>>>>>>> not to email before coffee...
>>>>>>>
>>>>>> Did you mean pull_group2_pbcatom? In my case:
>>>>>>
>>>>>> pull_group1_name        = K
>>>>>> pull_group2_name        = CNT
>>>>>>
>>>>>> The language for 5.1 pull is (you be the judge on how clear it is):
>>>>>>
>>>>>> pull-group1-pbcatom<http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#mdp-pull-group1-pbcatom> 
>>>>>>
>>>>>>
>>>>>>    (0) The reference atom for the treatment of periodic boundary
>>>>>>    conditions inside the group (this has no effect on the 
>>>>>> treatment of
>>>>>>    the pbc between groups). This option is only important when the
>>>>>>    diameter of the pull group is larger than half the shortest box
>>>>>>    vector. For determining the COM, all atoms in the group are 
>>>>>> put at
>>>>>>    their periodic image which is closest topull-group1-pbcatom
>>>>>> <http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#mdp-pull-group1-pbcatom>. 
>>>>>>
>>>>>>    A value of 0 means that the middle atom (number wise) is used. 
>>>>>> This
>>>>>>    parameter is not used withpull-group1-geometrycylinder. A 
>>>>>> value of
>>>>>>    -1 turns on cosine weighting, which is useful for a group of
>>>>>>    molecules in a periodic system,/e.g./a water slab (see Engin 
>>>>>> et al.
>>>>>>    J. Chem. Phys. B 2010).
>>>>>>
>>>>>> Indeed, my group2 is a membrane that is wider than the shortest 
>>>>>> half-box. I am assuming it would be a single atom belonging to 
>>>>>> the pore region...
>>>>>>
>>>>>
>>>>> Yes, pull_group2_pbcatom, not 1.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Alex
>>>>>
>>>>
>>>
>>
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