[gmx-users] t_trxframe speed units

aherz alexander.herz at mytum.de
Wed Sep 2 14:38:35 CEST 2009

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).


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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