[gmx-users] Regenerating tpr files

Justin Lemkul jalemkul at vt.edu
Thu Sep 5 12:05:07 CEST 2013

On 9/5/13 1:10 AM, Piduru Viswanath wrote:
> Hi,
> I have run my MD till 13 ns extending it by 500 ps simulations. But while
> shifting the data from a system, accidentally I lost my tpr files. My
> backup contains trr files till 13 ns (i.e. all trr files) and tpr files
> till 6.5ns. How could I regenerate the tpr files now if I have to extend
> the simulation further? While using tpbconv I received an error which
> prompted me to use cpt file. But I don’t have cpt files, Is there a
> solution to this problem?

The bigger problem is the .cpt files; you can't extend the simulations without 
them, at least not in the most rigorous way.  It's easy to re-generate a .tpr 
file, just re-run grompp.  The state information for a continuation is taken 
from a .cpt file, so that's the most important one for a restart.  If you've 
lost those as well, then you won't have an exact continuation.  You can probably 
continue from information in .trr and .edr files (i.e. the ancient way of 
restarting/continuing a simulation), but it will not be exact.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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