[gmx-users] t_trxframe speed units
gmx3 at hotmail.com
Wed Sep 2 14:00:37 CEST 2009
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.
> 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??
> 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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