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0 votes
by (160 points)
Dear devs,

I tried to use bench to do single cell pacing on the HodgkinHuxley model. I used this command:
/usr/local/bin/bench --duration 5000 --stim-assign on --imp HodgkinHuxley --stim-curr 50.0 --numstim 11 --bcl 500 --dt 0.01 --dt-out 0.1 --save-ini-file HodgkinHuxley_bcl_500_ms_dur_5000_ms_imppar_.sv --save-ini-time 5000 --fout=exp03/HodgkinHuxley --bin -v

However, When I plot the transmembrane voltages, it seems only the first pulse is able to excite the tissue. (links to images: https://drive.google.com/file/d/1a6ckuWipvlzIMv6SkQiRCp5nb823OOk_/view?usp=drive_link , https://drive.google.com/file/d/1R7rk7DF3f6abJE-nH1832PseewbLnDbY/view?usp=drive_link)

I tried a larger --stim-curr and --stim-volt, but this behavior persists. In addition, the shape of the first action potential looks very odd.

Any explanation on what I am doing wrong?

Kind regards,
Robin

2 Answers

0 votes
by (3.5k points)
Hi Robin,

I was not able to access the figures. Could you please check the rights?

Cheers,

Jorge
by (160 points)
Hi Jorge,

My apologies. I changed the permission. It should be visible now.
by (3.5k points)
Hi Robin,

Thanks! I will look into it and get back yo you as soon as possible.

Cheers,

Jorge
0 votes
by (3.5k points)
Hi Robin,

I updated the HodgkinHuxley.model in the openCARP repository. Please update your code to the latest state of the main. Let me know if you find something else in the model.

Cheers,

Jorge
by (160 points)
Hi Jorge,

I tried installing by compiling from source (I used .deb packages before), however, I get errors when I try to build opencarp either through cmake (left) or the makefile (right).
https://drive.google.com/file/d/1NAriFftsubBNXfDJlIxgTCSvgHRAqTmK/view?usp=drive_link

Everything seems to be correct in my bashrc file:
https://drive.google.com/file/d/16xkSWbOEI7HiTjB6nQZwIz-oD03Rqe1i/view?usp=drive_link
by (3.5k points)
Hi Robin,

It seems that you have two different versions of petsc.

Cheers,

Jorge
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