[gmx-users] direction_periodic

aherz alexander.herz at mytum.de
Mon Sep 21 14:42:43 CEST 2009


With master branch you mean the code I get via

|git clone git://git.gromacs.org/gromacs.git

right?

Alex
|



Berk Hess schrieb:
> 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.
>
> Berk
>
> > 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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