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

[Justin Lemkul]

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

-- 
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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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