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

Inon Sharony InonShar at TAU.ac.IL
Mon Jul 16 13:20:53 CEST 2012

   Correction -- in the first sentence:

   "... velocity coordinates (-ov) ..."

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

   On 07/16/2012 02:19 PM, Inon Sharony wrote:

     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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