The basics of how to develop, test, and use models.
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when I use SEClamp to perform an experiment, I usually got some small transient in the beginning of the simulation. But occasionally I got some very positive and very negative values (10 to the 4 order of magnitude bigger) at t=0 and it decays rapidly. Are they still transients? Is it possible to avoid them (or reduce)? Thanks!
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This means that your model is being initialized to a potential that is different from the value specified by the SEClamp's amp1 parameter. Compare the value of v_init and the SEClamp's amp1.manyi wrote:when I use SEClamp to perform an experiment, I usually got some small transient in the beginning of the simulation.
Some models--especially those that have nonuniform membrane properties, or involve ion accumulation--require a custom initialization to make sure that they are actually in the steady state; for these, the symptom of inadequate intialization will be a slow fluctuation of clamp current over the course of many milliseconds. Others don't have a steady state, and some of these may show periodic or erratic fluctuations of clamp current.