[gmx-users] Restart dynamics when trr files removed

Justin Lemkul jalemkul at vt.edu
Tue May 14 17:06:26 CEST 2019

On 5/14/19 10:34 AM, CROUZY Serge 119222 wrote:
> Hello Jon and Justin
> I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella simulations using pull code)
> I did try the -cpi option and my calculation seems to have restarted correctly renaming the files dyn.part0003....
> But just running
> gmx mdrun -cpi  -noappend
> does not allow me to tell the number of additional steps I want in my dynamics - So right now it's running 46 more ns (the original mdp and tpr file) which is not reasonable because I have 100s of calculations to run - I want to be able to specify 5 ns more for instance
> Usually I use gmx convert-tpr - extend 5000 which builds a new tpr with which I can restart with -cpi
> And running without a checkpoint file, Justin is not what I want - I really need to restart my dynamics after 46 ns, just I don't want the trr files - (I've got all the other files all right) - There should be a trick to restart without writing to a trr file... Isn't there ?

Any change to output frequency requires grompp to create a new .tpr and 
to start over as a new run. You can continue from the place you were via 
grompp -t .cpt with the last checkpoint you have. The subsequent mdrun 
will "continue" from the exact point in time but is not a "continuation" 
in the sense of using mdrun -cpi.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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