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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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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