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

Justin Lemkul jalemkul at vt.edu
Tue Mar 13 15:18:59 CET 2018

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.


> Thanks,
> Alex


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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list