Search found 9 matches

by agow
Sat Apr 29, 2017 5:48 am
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

followed your lead and found the additional updated channels (na12 and na16 from foutz et al) that i have been using. sadly the new channels have different kinetics so a straight substitution is not possible. will have to leave this for now and continue with fixed dt. thanks again.
by agow
Thu Apr 27, 2017 4:48 pm
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

Hi ted,
this is fantastic news. I looked for updates but i didnt find them. i will test them post haste. cheers and thanks again.
by agow
Sat Apr 22, 2017 5:28 am
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

Hi ted, just looking at the scope of this project and i suspect that a search for CVODE compatible mechanisms might take as long as i have to explore the model (a week or so). Accordingly i might just take this on the chin. I increased Atol stringency on a few runs and it seems to stabilize the solu...
by agow
Thu Apr 20, 2017 5:35 am
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

looking at the mod files, i see they are built by Zach Mainen and Alain Destexhe in the mid 90s. thanks for your help.
by agow
Wed Apr 19, 2017 5:17 pm
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

i am running nrn-7.4 on a Core2 vPro machine and windows 7 enterprise. i tested your recommended sequence with NEURONdemo and obtained the pop up window. not so lucky loading my own myelinated neuron. Clicking the use variable dt checks the box. Clicking the Atol scale tool button is acknowledged in...
by agow
Wed Apr 19, 2017 2:57 pm
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

just checked with the Neuron book and daspk should work for me. i am running the extracellular mechanism to simulate myelin on the axon. just checking that the numerical method selection is operating correctly. when i open the dialog from the variable timestep window, i can select daspk but i cannot...
by agow
Wed Apr 19, 2017 12:49 pm
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

OK works now. i must have attempted adjusting dt in the wrong way. unfortunately i still see the oscillation using 973 points plotted / ms so the only option seems to be finding daspk compatible channels or figuring out how to convert them. any pointers here?
thanks
by agow
Wed Apr 19, 2017 5:11 am
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

Re: dt resolution and unexpected oscillations

thanks for your suggestions. would love to use daspk just because of the simulation time savings. unfortunately several of the ion channel mechanisms i obtained from modelDB are only compatible with the fixed time step. i cant read or script in hoc so i am unable to solve the problem. is there a con...
by agow
Tue Apr 18, 2017 4:35 pm
Forum: The GUI
Topic: dt resolution and unexpected oscillations
Replies: 14
Views: 9119

dt resolution and unexpected oscillations

i have been testing a single neuron generated with cellbuilder, which includes an axon initia segment so i can explore the effect of changing ion channel densities on the max amplitude of back propagating action potentials (bAPs). i was intrigued by an unexpected oscillation in bAP amplitudes while ...