[gmx-users] Extending a simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 17 17:24:55 CEST 2012

Shyno Mathew wrote:
> Dear all,
> This is the first time I am trying to extend a run in gromacs.
> I read in the gromacs website following are the steps to used for this 
> purpose:
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
> So this means I don't need to modify the .mdp file at all?


> For instance, what about these two parameters: tinit, continuation
> I thought tinit has to be changed to time last time step of previous run 
> and continuation has to be set to 'yes'.

The only time you have to use .mdp files for continuation is if you are changing 
some aspect of the ensemble, output control, etc.  Tutorials have you deal with 
the continuation parameter, for instance, when moving between different steps in 
equilibration.  That is because you are changing the ensemble (NVT, NPT, etc) 
and thus you cannot do a simple extension of the simulation.  For production 
simulations that simply require more time, the steps listed on the Gromacs 
website are correct and there is no need to deal with .mdp files.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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