Correction -- in the first sentence: "... velocity coordinates (-ov) ..."
Inon Sharony J+N+W+N% ShR+W+N+J+ [1]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 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+ [2]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 References Visible links 1. http://atto.tau.ac.il/~InonShar 2. http://atto.tau.ac.il/%7EInonShar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
