[gmx-users] empty velocity *.xvg file from g_traj

[Jochen Hub]

Inon Sharony wrote:
> 
>  Good morning!
> 
> Firstly, I'd like to thank congratulate everyone involved for ver 4.0
> 
> 
> Now for business:
> 
> I'm getting empty *.xvg files from g_traj... this doesn't always
> happen, and I can't find what I'm doing differently... I'm running
> version 3.3.3 on Ubuntu:
> 
> --------------------------------------------------------------------------------
> 
> 
> grompp_d -f eq -c b4eq -n -t
> mdrun_d -c b4md -v
> 
> grompp_d -f md -c b4md -n -t
> mdrun_d -c md -v
> 
> g_traj_d -n -ox x_ndxgrp1 -ov v_ndxgrp1
> 
> --------------------------------------------------------------------------------

By default, g_traj reads the traj,xtc (check g_traj -h) which does not
contain velocities. Have you tried g_traj_d -f traj.trr ?

Jochen



> 
> 
> gives me two *.xvg files:
> the x_ndxgrp1 file is fine, but v_ndxgrp1 has an xmgrace formatting
> header, and then no data afterward. This formatting information agrees
> with the number of atoms in the group ndxgrp1.
> 
> what am I doing wrong?
> 


-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************