[gmx-users] t_trxframe speed units

[Berk Hess]

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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