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

[Silvia Di Lecce]

Hi Tsjerk,
I have written g_traj -n index.ndx -f traj.trr -s topol.tpr and it works.
Thank you for your prompt reply.
Best,
Silvia



2013/7/2 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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
> >
> >
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/Cannot-get-velocities-from-the-trajectory-file-tp5009511.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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