What determines the time step of rule based simulation

[Kun]

Hello, I noticed that when running the rule based simulations, the time interval between two steps is not uniform. Why is this? I'm new to this and maybe this is a stupid question, so I would also appreciate if some documents are recommended so that I can figure out myself.

Thanks a lot

[Blinov,Michael]

The default simulation output keeps non-uniform time points to allow all features of the time-course to be tracked - more timepoints for stiff solutions, less points for steady. There is an option to change the output to uniform time points:

Simulations -> Edit Simulation -> Solver -> Output Options -> Output Intervals. 

Uniform time points are great for comparing multiple simulations, but they can miss some very stiff features of the solution (e.g. oscillation with a small period may be lost).

Best,

Michael

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Subject: [VCell] What determines the time step of rule based simulation

 

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Hello, I noticed that when running the rule based simulations, the time interval between two steps is not uniform. Why is this? I'm new to this and maybe this is a stupid question, so I would also appreciate if some documents are recommended so that I can figure out myself.

Thanks a lot

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[Kun]

Got it! Thanks for the explanations!

Best,

Xikun