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 region...


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