[gmx-users] direction_periodic

Berk Hess gmx3 at hotmail.com
Mon Sep 21 14:38:39 CEST 2009

I tested on your system and got good results.
There is still a tricky issue: the pull COM is still determined
in the "standard" way by summing distances from the pbcatom.
Therefore atoms should not change nearest image from he pbcatom.
This would result in nasty noise in the pull COM and force.

I would suggest that you try to run the master branch and check
if that works.


> Date: Mon, 21 Sep 2009 14:31:34 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] direction_periodic
> Hey,
> after some pain of merging the dev branch into our 4.0.5 version I got
> the new pull mode "direction_periodic"
> running over the weekend. There's some weird rotation of the pulled
> objects going on and pbc seem weird as well (there are water molecules
> in those positions where I'd expect the periodic image of my diamond
> slab which leaves the box at one side). I guess you tested the new pull
> mode somehow, so any ideas what's going on here? I'm still trying to
> perform the same experiment for which I send you the input files while
> ago and for which you kindly implemented the new pull mode.
> Thx for your help,
> Alex
> Berk Hess schrieb:
> > I have committed a new pull geometry direction_periodic to the git
> > master branch. It is not documented yet.
> > It works the same at direction, but allows distances to be larger
> > than half the box and does not add the pull force to the virial.
> >
> > Berk
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