www.neuron.yale.edu

Since you're working with hoc, you should read this ASAP: Hines, M.L. and Carnevale, N.T. The NEURON Simulation Environment Neural Computation 9:1179-1209, 1997. https://neuron.yale.edu/neuron/static/papers/nc97/nctoc.htm You might want to download the preprint, which is available from a link on tha...

The answer is "don't". That's a lousy user interface--it's inconvenient, tedious, prone to user error, not very readable, and guarantees irreproducibility ("now, what command line did I use to get this interesting result?"). And it's a great way to make sure that nobody else wants to use your code. ...

Good question. Many people make similar mistakes. Here's a chance to learn a lot. What am I doing wrong? Misdiagnosing the cause of the problem because of failure to localize the problem. In medicine, the first step in diagnosis is to localize the cause of the problem. This is also true for diagnosi...

I'm trying to download the old version of NEURON5.9 in order to run a legacy model, but I'm not quite sure about which folder should I download from https://neuron.yale.edu/ftp/neuron/versions/v5.9/ There are no folders at that location. Download the installer that is appropriate for your hardware ...

This is not a problem of "magic numbers." There's a bug, either a subtle syntax error in your NMODL code or in NEURON itself. I'll need to work with your NMODL file in a toy model. If the NMODL file can be used by itself in a single compartment model, that's all I'll need. If it requires other mecha...

Brilliant up to a point. The NMODL source code will tell you the default values of parameters. However, it won't tell you the actual value of any parameter used in a particular model implementation, because those can be changed by hoc or Python assignment statements. Also, if mechanism X's PARAMETER...

I'd suggest changing
SOLVE blrrate METHOD cnexp
to
SOLVE blrrate METHOD derivimplicit
because many of the state variables have very small values and should not become negative.

mech contains parameters like 'gbar', 'g', 'ica' and so on. Not what I see. Given soma = h.Section(name='soma') soma.insert('hh') then for seg in soma: for mech in seg: print(mech) returns k_ion na_ion hh but no mention of gnabar, gkbar, gl. or el, which are declared in hh.mod's PARAMETER block.

Does the STATE block declare all of the variables that appear on the LHS of the ODEs?
What are the contents of the BREAKPOINT block?
Is initialization of the state variables correct?
Is PROCEDURE calcparameters() working properly?

If you're not planning to use Python with NEURON or vice versa, ignore the message. Otherwise, uninstall NEURON completely--COMPLETELY--and then reinstall and accept the "add python to path" option.

Are there some other ways that I can run this model without using cmd Nope. after removing the statement { neuron_name = "d151" , I double-clicked the eaps\cells\d151.hoc file and successfully got the shape plot. cell_type = "ca1pyr" } Then I tried to load other hoc files from Neuron Main Menu\File...

if I calculate single channel current's (implemented as point-process) contribution to LFP As a point process? What does point process have to do with anything? Most voltage-gated channels are implemented as density mechanisms. The currents they generate have units of mA/cm2 and must be multiplied ...

At large distances (more than about 10 x segment length) it is reasonable to treat the segment as a point source of current located at the segment center. A more fastidious approach is to treat each segment as a line source with the same length as the segment, centered at the location of the segment...

Sure. Forget about Windows. Use Linux instead. The code runs without complaint under Linux. Making it work under Windows is going to be a major pain.

Assuming that one or more cells are embedded in a conductive medium that is linear, the potential Vi at any point i in the medium is Vi = SUMMA Zx_j Im_j j where the index j ranges over all compartments in the model, Im_j is the total (i.e. ionic + capacitive) transmembrane current for compartment j...