[gmx-users] Re: Extending a run and changing nstxout

Andrew DeYoung adeyoung at andrew.cmu.edu
Fri Jul 27 17:31:14 CEST 2012


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
> 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
> last checkpoint file saved in the original run.  (The -noappend option
> that the additional 10 ns (t = 10 ns to t = 20 ns) will be put in a
> .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
> 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.


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