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

[Alex]

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?

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
>