Chapter 8. Simulation Control and Plotting

8.1 Simulation Control

Pressing the "Run Control" on the main menu brings up a Run Control panel designed to make the control of simulation runs very convenient for the user. It is a minimal control system for managing a single "Oscilloscope sweep" level of simulation runs.

The "Init" button in this panel will initialize all of the simulation states to the initial voltage level (vinit) displayed in the value editor. It executes the procedure called "init()" shown below:

 proc init()    {finitialize (v_init)   fcurrent()}

The "Init & Run" button in this panel carries out

The same processes could be carried out by typing both "init()" and "run()" in the hoc interpreter window.
The"Stop" button will halt a simulation at the end of a step, but it can be resumed by pressing any one of the next three buttons:

  • "Continue til" button to continue the simulation until "t" reaches the value in the "Continue til" vlaue editor, or the
  • "Continue for" button to continue the simulation for the number of milliseconds in the "Continue for" value editor or
  • "Single Step" button to continue the simulation for one time step.
  • Control of Timing parameters

    "t" , NEURON time, is displayed in milliseconds. It is updated (incremented by "dt") at each time step.
    "Tstop" determines the time at which the simulation normally terminates.
    "dt" Is the value of the fundamental integration time step.

    Its default value was chosen as 25 micro Seconds - an excellent compromise between speed and accuracy - and need be changed only rarely. However, some complex simulations may require a small dt for accurate results. When another value is entered into the field editor, it is rounded down so that an integral multiple of fadvances's make up a "Single Step".

    "Points plotted/ms" sets the number of times NEURON updates the graphs per millisecond. The default value of 40/mS (a point plotted at each "dt") offers a compromise between the "smoothness" of the plots and the CPU time used for the simulation. Because generation of graphs during the simulation run often takes much more time than the calculations, decreasing this number will speed the simulation at the expense of increased "graininess" in the plots. The overall simulation time "Real Time" is shown in the "NEURON Main Panel" .

    Notice that: