[gmx-users] Re: Extending a simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 18 20:21:56 CEST 2012

Shyno Mathew wrote:
> Hello,
> Thank you very much for your replies Mark and Justin.
> with -deffnm option I can see all the data are written to my previous files.
> one final question related to this topic:
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> Is  the 'timetoextendby' the actual time or 'nsteps'? For example in the 
> .mdp file I have the time step as 0.002 and I want to extend the 
> simulation by 50 ns.
> so should I put timetoextendby as '50000000' or '25000000'?

Neither - 50 ns is 50000 ps, not 50000000 ;)

 From tpbconv -h you will see:

-extend      real   0       Extend runtime by this amount (ps)

Alternatively, one can use -nsteps, which changes the *total* number of steps 
(not just adding on to the end).



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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