[gmx-users] Cannot get velocities from the trajectory file

Silvia silviadilecce.s at gmail.com
Tue Jul 2 20:25:04 CEST 2013

Dear users and experts,
I am new in the list and I am writing because I have a problem to get
velocities from the trajectory file. When I use this command line g_traj -n
index.ndx -s topol.tpr -f traj.xtc -ov, I obtain the veloc.xvg file but
there is no data inside. I have the same problem on the force.xvg (-of) file
but not on the coord.xvg one (-ox). So there is no information about the
velocities and the forces in the trajectory file. I enclose the output
parameters of my *.mdp file.

integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 2500000
; For exact run continuation or redoing part of a run
init_step                = 0

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 1000
nstcalcenergy            = -1
nstenergy                = 1000
; Output frequency and precision for .xtc file
nstxtcout                = 1000
xtc-precision            = 1000
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                 =
; Selection of energy groups
energygrps               =

Can someone help me to solve this problem?
Thank you in advance.


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