[gmx-users] t_trxframe speed units

[Berk Hess]

I don't understand what you want to say.
The diamond does move a lot right?

I think the main problem might be that you use an umbrella potential
will an very small force constant (for such large groups).
Try using pull=constraint.
(and use pull_start=yes)

Berk

> Date: Wed, 2 Sep 2009 15:22:45 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] t_trxframe speed units
> 
> 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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