<PSICSRun timeStep="0.01ms" runTime="20ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="1000"
	repeats="400">
	<StructureDiscretization baseElementSize="3um"/>

<RunSet vary="napop:density" values="[2, 4, 8, 16]per_um2"
                filepattern="out-$">
	</RunSet>



<About>
 Voltage clamp with stochastic channels. There are four cases varying in
  the density of channels in the model (from 2 or
  to 16 per square micron).  Each case is run 400 times of which six are
  shown in the default plots. The mean variance analysis operates on the
  5-10 ms time window and shows the variance against the mean current. The form
  should be a parabola, with the slope at the origin giving the single channel
  conductance and the intercept on the X axis the total number of channels.
 </About>



	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>

		<LineSet file="out-2.txt" color="red" maxshow="6"/>
		<LineSet file="out-4.txt" color="orange" maxshow="6"/>
		<LineSet file="out-8.txt" color="blue" maxshow="6"/>
		<LineSet file="out-16.txt" color="green" maxshow="6"/>


		 <View id="whole" xmin="0." xmax="25." ymin="-160." ymax="20."/>
		</LineGraph>


		<LineGraph>
			<XAxis label="mean current, nA"/>
			<YAxis label="current variance, nA^2"/>
				<MeanVariance file="out-2.txt" tmin="5" tmax="10" binSize="1" color="red"/>
			 	<MeanVariance file="out-4.txt" tmin="5" tmax="10" binSize="2" color="orange"/>
			 	<MeanVariance file="out-8.txt" tmin="5" tmax="10" binSize="10" color="blue"/>
	        	<MeanVariance file="out-16.txt" tmin="5" tmax="10" binSize="20" color="green"/>

	            <View id="mvwhole" xmin="0" xmax="250" ymin = "0." ymax="200"/>
		</LineGraph>


	</ViewConfig>


</PSICSRun>

<CellMorphology id="cell">

    <Point id="p0" x="0" y="0" z="0" r="1."/>

</CellMorphology>

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1.e-8uF_per_um2">

	<ChannelPopulation id="napop" channel="na1" density="16per_um2"/>


</CellProperties>

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="80mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

<Access id="recording" saveInterval="0.05ms">

	<VoltageClamp at="p0" lineColor="red" hold="-80.0mV">
		<VoltagePulse id="vstep" start="5ms" to="0mV"
			      duration="12ms"/>
	</VoltageClamp>

</Access>

<KSChannel id="na1" gSingle="30pS" permeantIon="Na">
	<ClosedState id="c1"/>
	<OpenState id="o1"/>
	<ClosedState id="c2"/>

	<VHalfTransition from="c1" to="o1" vHalf = "-35mV" z="4.5e" gamma="0.8" tau="0.55ms" tauMin="0.1ms"/>

	<VHalfTransition from="o1" to="c2" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="12.0ms" tauMin="1.5ms"/>

</KSChannel>