[gmx-users] Positions and velocities from trajectory for restart

Inon Sharony InonShar at TAU.ac.IL
Mon Jul 16 13:19:31 CEST 2012

   Good afternoon.

   g_traj has the option to output position coordinates (-ox) OR velocity
   coordinates (-ox) from an input trajectory file. The former can even be
   output to a trajectory file format, trr/trj/cpt (-oxt). I would like to
   restart a simulation using a separate set of MD parameters (mdp) from the
   phase-space point in a given time frame of a previous trajectory. I need
   BOTH position and velocity coordinates to fully reproduce the system in
   phase-space. Non of the above cited options suffice, since they give me
   only one of the two (positions OR velocities) but not both.

   Ideally, I would like to use something like

   g_traj -f traj-old -s topol -b $t_init -e $t_final -ot traj-new -fp

   To create a new trajectory file "traj-new.trr" which contains both
   positions and velocities which appear in "traj-old.trr" between
   time-frames $t_init and $t_final (this could be only one time-frame),
   where the currently non-existent g_traj option "-ot" outputs both
   positions and velocities from one trajectory to another. Is there a way to
   do this now? If not, could you possibly implement such an option?

   From the GMX website I understand that re-starting simulations is being
   pushed towards using checkpoint (cpt) files rather than trr. However, when
   I tried to see if the velocities get copied to the cpt file, I got:

   $ echo 0 | g_traj_d -f traj.trr -s topol.tpr -oxt traj.cpt -fp

   \001\001 "Source code file: trxio.c, line: 269
   \001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt"

 Inon Sharony J+N+W+N% ShR+W+N+J+


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