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

[Tsjerk Wassenaar]

Hi Silvia,

The .xtc file does not contain velocities. You'll need to use the .trr file.

Cheers,

Tsjerk


On Tue, Jul 2, 2013 at 8:25 PM, Silvia <silviadilecce.s at gmail.com> wrote:

> 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.
>
> ; RUN CONTROL PARAMETERS
> 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 CONTROL OPTIONS
> ; 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.
>
> Silvia
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.