Hi, Thanks, Justin! Is it possible to set the start time as t = 10 ns instead of t = 0? When I pass the checkpoint to grompp with -t, the simulation starts at t =0 by default. Is there a way to change this, such that I will be able to easily concatinate the two trajectories using trjcat (i.e., concatinate t=0 ns to t=10 ns and t=10 ns to t=20 ns) if needed?
Andrew DeYoung Carnegie Mellon University > Hi, > > I would like to extend a run. I ran a 10 ns simulation, and I would like to > run the simulation for an additional 10 ns. Normally I would do this with > the following two commands: > > tpbconv -s topol_old.tpr -o topol_new.tpr -extend 10000 > mdrun -cpi checkpoint_old.cpt -s topol_new.tpr -noappend > > where topol_old.tpr is the original .tpr file and checkpoint_old.cpt is the > last checkpoint file saved in the original run. (The -noappend option means > that the additional 10 ns (t = 10 ns to t = 20 ns) will be put in a separate > .trr file.) > > However, I am running out of disc space and I would like to reduce the > frequency with which I save configurations; I would like to use nstxout = > 200 instead of nstxout = 50 as in the original run. Is there any way that I > can use tpbconv or a similar utility to change the value of nstxout in > topol_old.tpr? > Use grompp with the desired output settings, passing the .cpt file to the -t flag to preserve the ensemble. -Justin -- 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
