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minimization not converged with charged termini
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2 years 6 months ago - 2 years 6 months ago #9179
by nanogod
minimization not converged with charged termini was created 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
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: 2 years 6 months ago by nanogod.
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2 years 6 months ago #9180
by nanogod
Replied by nanogod on topic minimization not converged with charged termini
BTW I use martinize v 2.6.3 modified to python3
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