[gmx-users] Positions and velocities from trajectory for restart
jalemkul at vt.edu
Mon Jul 16 14:21:08 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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