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

Alex nedomacho at gmail.com
Tue Mar 13 15:17:49 CET 2018

>> 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):


    (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
    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 



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