[gmx-users] t_trxframe speed units

[aherz]

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.
> > I get an avrg speed of 1.2 [nm/ps], so this is not just some
> fluctuation (last time I only looked at the last frame output by gromacs).
> >
> > t_trxframe::v contains the speed in [nm/ps] right?
> >
> > Could someone please comment on this? Why are the diamonds considerably
> > faster then the pull speed pull_rate1??
> > This is gromacs4.0.5 by the way.
> > Thx,
> > Alex
> >
> > using still this setup:
> >
> > Here is the pull setup:
> > pull = umbrella
> > pull_geometry = direction
> > pull_ngroups = 1
> > pull_group0 = DIAM
> > pull_group1 = DIAM2
> > pulldim = Y Y Y
> > pull_k1 = 1000.0
> > pull_rate1 = 0.01
> > pull_vec1 = -1.0 0.0 0.0
> >
> > and following geometry:
> >
> > box_z_max
> > water_slab
> > diam1
> > water_slab
> > diam2
> > box_z_min
> >
> > rest of the mdp:
> > title = 2 diamond surfaces
> > cpp = /usr/bin/cpp
> > integrator = md
> > nsteps = 2500000
> > nstlist = 50
> > nstxout = 50
> > nstvout = 50
> > nstxtcout = 0
> > nstlog = 1000
> > dt = 0.002
> > constraints = h-bonds
> > nstenergy = 100
> > ns_type = grid
> > coulombtype = pme
> > fourierspacing = 0.12
> > pme_order = 4
> > rlist = 0.8
> > rvdw = 0.8
> > rcoulomb = 0.8
> > tcoupl = berendsen
> > tc_grps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL
> > energygrps = DIAM DIAMCNST DIAM2 DIAMCNST2 SOL
> > tau_t = 0.4 0.4 0.4 0.4 0.4
> > ref_t = 300 300 300 300 300
> > compressibility = 0.0 4.5E-5
> > tau_p = 1.0 1.0
> > ref_p = 1.0 1.0
> > Pcoupl = berendsen
> > Pcoupltype = semiisotropic
> > gen_vel = no
> >
> >
> >
> >
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