[gmx-users] t_trxframe speed units

aherz alexander.herz at mytum.de
Wed Sep 2 14:11:11 CEST 2009

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)??


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.
> If your slabs are very rigid, you might be lucky that it works
> when you choose pull_pbcatoms for both groups that do not separate
> more than half a box.
> But this experiment is much simpler with a single diamond slab
> and the deform option to shear the box.
> You can get the force from the off-diagonal pressure element.
> Berk
>> Date: Wed, 2 Sep 2009 13:40:48 +0200
>> From: alexander.herz at mytum.de
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] t_trxframe speed units
>> I'm studying shear flow, so I exspect the two slabs to be pulled in
>> opposite x direction with the pull speed given.
>> Looking at pull.xvg the slabs are pulled apart with about 1.5nm/ps until
>> the box end (in x) is reached, then they jump back due to pbc. So this
>> is what I would exspect, exept that the speed is much too high.
>> hm..looking at the com speed vs time as per "g_traj -com -ov -n" for the
>> first diamond slab only,
>> the speed keeps increasing (see attached screenshot). Have I enabled a
>> non constant pull rate somehow??
>> Alex
>> Berk Hess schrieb:
>>> Hi,
>>> Yes, speed is in nm/ps.
>>> g_traj -com -ov -n will give the the speed of the slabs as a function
>>> of time.
>>> If the speed is really 1.2 nm/ps, they should have moved 6 nm in 5 ns,
>>> which is probably not the case, right?
>>> Could it be that you have pbc issues?
>>> The distance between the two slabs could be taken within the box
>>> or over the boundaries.
>>> Have a look at pullx.xvg to see if it does what you expect.
>>> (the time derivative of pullx.xvg should also give the speed
>>> difference of the slabs).
>>> Berk
>>>> Date: Wed, 2 Sep 2009 11:39:22 +0200
>>>> From: alexander.herz at mytum.de
>>>> To: gmx-users at gromacs.org
>>>> Subject: [gmx-users] t_trxframe speed units
>>>> Hey,
>>>> I averaged the speed of the diamond slabs, so I wrote a small gmx
>>> tools which averages t_trxframe.v[i] where i iterates over the diam atoms.
>>>> I calc the avrg speed for a production run of 5ns after 0.5ns equilib
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