On 7/16/12 7:19 AM, 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?


The -ot option is not non-existent, it's just unrelated to what you want to do, and it does not write a trajectory.

"Option -ot plots the temperature of each group, provided velocities are
present in the trajectory file. No corrections are made for constrained
degrees of freedom! This implies -com."

    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"


Does the -oxt option work to produce a .trr file? If you just want individual states from which to continue the simulation, you don't need g_traj at all. Just use trjconv -dump to drop out individual frames from the .trr file, which will contain coordinates and velocities present in the .trr file.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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