[gmx-users] GMX 2018 and 'distance' pull
jalemkul at vt.edu
Tue Mar 13 15:18:59 CET 2018
On 3/13/18 10:17 AM, Alex wrote:
>>> 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...
Yes, pull_group2_pbcatom, not 1.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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