[gmx-users] t_trxframe speed units

[aherz]

hm..

after thinking about this for a sec I'd say I'm missing an option to
apply the pbc to the pull position.
Currently it looks as if the position of the "afm tip" is moving in
absolute coordinates further and further away from the original position
while the diamonds stay in the original box due to applied pbc.
Therefore the distance of the diamond to the
"afm tip" is increasing and hence the force grows bigger and bigger. If
I could apply the pbc to the afm position as well then
everything would work as expected??

Alex

Berk Hess schrieb:
> Then you were lucky with Gromacs 3.
> The pull code in Gromacs 3 does not treat pbc at all,
> so I am surprised that it worked.
>
> I just realized that pull_pbcatom is always set in Gromacs 4.
> Maybe it would be enough to add pull_start=yes.
>
> Berk
>
> > Date: Wed, 2 Sep 2009 14:38:35 +0200
> > From: alexander.herz at mytum.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] t_trxframe speed units
> >
> > I will try this, thx for the help.
> >
> > Anyways, what is the correct way to do what I want with gromacs 4?
> > (apparently the setup I tryed to use worked for gromacs 3, since I
> > ported the input data
> > from old sims and now I'm trying to recreate the old results).
> >
> > Alex
> >
> > Berk Hess schrieb:
> > > The simple issue is that a center of mass is not uniquely defined
> > > for a periodic group of particles.
> > > If you work on the velocity level, this problem is easy to solve.
> > > But the pull code works on the coordinate level.
> > >
> > > Try with pull_pbcatom set, it might work.
> > >
> > > Berk
> > >
> > >
> > >> Date: Wed, 2 Sep 2009 14:11:11 +0200
> > >> From: alexander.herz at mytum.de
> > >> To: gmx-users at gromacs.org
> > >> Subject: Re: [gmx-users] t_trxframe speed units
> > >>
> > >> We wanted to use 2 slabs so that the net impuls is conserved.
> > >> Also I'm looking at the slip length, so I actually want to
> extract the
> > >> velocity profile of the water in between the two diamond slabs. I'm
> > >> pulling in x (the pull setup is reproduced at the bottom of the old
> > >> mail) and I'm using pbc in 3d.
> > >>
> > >> What is the problem with pulling the diamond slabs at const speed? I
> > >> don't actually care where exactly they are.
> > >> I only care about the boundary condition at the diamond water
> interface
> > >> (so that the diamond moves along the surface
> > >> with v=cst). I mean, I'm pulling with "direction" not distance,
> why does
> > >> "direction" care about the COM distance?
> > >>
> > >> Would it work with absolute coords (empty pullgroup0,
> pullgroup1=DIAM1
> > >> and pullgroup2=DIAM2)??
> > >>
> > >> Alex
> > >>
> > >> Berk Hess schrieb:
> > >>
> > >>> Ah, maybe now I understand the issue.
> > >>> Are you pulling in x and are the slabs periodic in x?
> > >>> That will not work, as the COM is not defined in a periodic
> direction
> > >>>
> > >>>
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