[gmx-users] Restart dynamics when trr files removed

Justin Lemkul jalemkul at vt.edu
Mon May 13 15:57:36 CEST 2019

On 5/13/19 8:20 AM, CROUZY Serge 119222 wrote:
> Dear Gromacs users
> I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files
> Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new
> gmx grompp and corrected mdp file (with nstxout=0)...
> But NO - I can't restart the simulation  from 50 ns on without trr files - Whatever tricks I seem to have tried to fool the controls
> I hope someone can tell me how I can solve my problem  - Even if it is recompiling the source to remove the flag checking
> that the trr file is absent

A new run using grompp and mdrun without a checkpoint file should not 
complain about missing files, because it is a new run and the check is 
only done when using mdrun -cpi. Even with mdrun -cpi, if you use 
-noappend, it should also not look for files to which it needs to append.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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