[gmx-users] direction_periodic

Mon Sep 28 15:40:16 CEST 2009

Hey,

so using the new direction_periodic with some kernels that actually work
and the sources from the git (unmodified)
gives a nice smooth pull force but no actual mean displacement of the
groups to be pulled (on average they just stay where they are,see
attached graph). I'm still trying to pull them into opposite directions
though.

I'm using this setup:
pull            = umbrella
pull_geometry   = direction_periodic
pull_ngroups         = 1
pull_group0          = DIAM
pull_group1          = DIAM2
pulldim         = Y N N
pull_k1          = 1000.0
pull_rate1       = 0.01
pull_vec1        = -1.0 0.0 0.0

How can I make the two diamond slabs actually move in opposite
directions rather than just oscillating around their
initial positions?

Thx,
Alex

Berk Hess schrieb:
> Hi,
>
> Don't use fortran.
> We will get rid of it before the 4.1 release.
>
> Berk
>
> > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > From: alexander.herz at mytum.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > ok, I checked this. It works ok with the assembly kernels on my local
> > machine, but it fails with fortran kernels
> > on the HPC and on my local machine.
> >
> > Alex
> >
> > Berk Hess schrieb:
> > > Yes.
> > >
> > > Berk
> > >
> > > > Date: Mon, 21 Sep 2009 14:42:43 +0200
> > > > From: alexander.herz at mytum.de
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] direction_periodic
> > > >
> > > > 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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