[gmx-users] t_trxframe speed units

[aherz]

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