Time step for simulations

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Luciana Renata de Oliveira

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Feb 2, 2021, 6:46:41 AM2/2/21
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Hello, 
I am a new user of kappa and I would like to change the time step for the simulation.
Is that possible?

Thank you.

Luciana

Walter Fontana

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Feb 2, 2021, 11:39:08 AM2/2/21
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Hi Luciana

A continuous time Markov Chain (Gillespie) has no time "step". The time interval to the next event is determined by an exponential probability density whose parameter is the sum of all rule activities. Please see section 3.4 of the manual(-in-progress...) and appendix D therein, or any number of review papers on the Gillespie algorithm. Why do you think you need to set a time step?

Best
w

yarde...@gmail.com

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Feb 3, 2021, 9:19:41 AM2/3/21
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The stochastic simulation has no time step, as Walter noted, but KaSim does have a time step setting for reporting the results. The parameter is called "plot period" and you can set it on the command line with "-p". Perhaps this is what you were looking for? Best, Yarden
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