[gmx-users] t_trxframe speed units

Berk Hess gmx3 at hotmail.com
Wed Sep 2 14:18:30 CEST 2009

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.


> 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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