I am running Rallpacks benchmark (http://www.ncbi.nlm.nih.gov/pubmed/1281353) with Neuron. The reference benchmark came with NEURON and GENSIS scripts. I modified the NEURON script for NEURON7.x.
The reference contains a cable with 1000 compartments. Each compartment having HH-type Na and K channels. A pulse of 0.1nA is applied to one end and membrane potential is recorded at both ends. This is how the result looks like in benchmark.
When I simulate it using NEURON-7.3 on Linux/i686. I get the following difference. The latest NEURON generates slightly faster action potential.
I was not expecting to see any difference. I am not sure why this is happening. Has anything changed in H-Solve? The MOOSE simulator is producing results comparable to reference.
Since I had to modify the original script, I am posting the script I used to simulate it.
Code: Select all
dia = 1.0
len = 1.0
incompts = 1000
entire_len = incompts * len
runtime = 250.0
create cable
access cable
nseg = incompts
/*
** Initialization routines
*/
cable {nseg=incompts L=entire_len diam=dia insert hh}
proc geometry() {
L = entire_len
diam = 1
Ra = 100.0
}
proc membrane() {
insert hh
ena = 50
ek = -77
el = -65
gnabar = .12
gkbar = .036
gl = 1 / 40000
cm = 1
}
/*
** Simulation and output of data
*/
proc run() { local io
geometry()
membrane()
v = -65.0
t=0
m = m_hh
h = h_hh
n = n_hh
dt = 0.05
io = 0
wopen("cable.out")
fstim(1) fstim(0, 0, 0, 251, .100)
fprint("%g %g %g\n", t, v(0.0005), v(0.9995))
while (t < runtime) {
fadvance()
fprint("%g %g %g\n", t, v(0.0005), v(0.9995))
}
wopen()
}
run()