[gmx-users] continuation options

Berk Hess gmx3 at hotmail.com
Tue Nov 11 15:39:49 CET 2008

> From: larsson at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Date: Tue, 11 Nov 2008 14:50:46 +0100
> Subject: [gmx-users] continuation options
> With Gromacs 4.0 I get this message:
> NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
> tpbconv can not provide binary identical continuation.
> If you want that, supply a checkpoint file to mdrun
> Is it possible to extend a trajectory with mdrun, a checkpoint file  
> and a new tpr-file? E.g:
> tpbconv -s original.tpr -f original.trr -e original.edr -o  
> extension.tpr -extend 10000
> mdrun -s extension.tpr -cpi original.cpt

Simply do not supply the trr and edr to tpbconv.
mdrun does not read the state from the tpr file, but from the checkpoint file
when you give the -cpi option to mdrun.

> Wouldn't it be nice if one could feed tpbconv with a checkpoint file  
> to generate a tpr file?

Yes, but then the tpr file should contain the whole state.
You now never need to create a new tpr file,
unless you want to make the run longer than you orginally thought.


> - Daniel
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