normal minimization not converged with charged termini

  • nanogod
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1 month 3 weeks ago - 1 month 3 weeks ago #9179 by nanogod
Hi Martini super users :)

I am having trouble with martini2.3p (I mean to switch to martini3 when i get time to learn the methods). I am trying to mimic a high pH environment where amino acids are negatively charged but not positively charged.

For all other amino acids but the termini this is fine. However, when I dont use -nt together with the martinize.py script I get minimization on converged and if I continue to a MD simulation I get lincs warnings and a crash. When I do use -nt everything is fine.

I noticed the charge og the termini is located at the BB and not with a dummy molecule. Might this be an explanation?

BTW I use martinize v 2.6.3 modified to python3

br
Morten
Last edit: 1 month 3 weeks ago by nanogod.

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1 month 3 weeks ago #9180 by nanogod
BTW I use martinize v 2.6.3 modified to python3

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