[gmx-users] t_trxframe speed units
gmx3 at hotmail.com
Wed Sep 2 14:45:59 CEST 2009
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.
> 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).
> 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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