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

Alex nedomacho at gmail.com
Tue Mar 13 15:32:17 CET 2018

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?



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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