[gmx-users] Extending a run and changing nstxout

Justin Lemkul jalemkul at vt.edu
Fri Jul 27 04:06:58 CEST 2012

On 7/26/12 9:59 PM, Andrew DeYoung wrote:
> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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