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unanswered Bent helices causing backbone to explode

  • Trayder
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7 years 11 months ago #5597 by Trayder
Bent helices causing backbone to explode was created by Trayder
Hi,
I'm running a simulation of a helical protein interacting with lipids.
I've defined my entire protein as helical and in a water box it favors a conformation with a mostly linear helix. When I introduce small micelles into my system the protein wraps around them (as expected) and the protein backbone frequently explodes at the resultant hairpin turns.
These explosions still occur when I lower the timestep to 10 fs.

Is there anything I can do to make these simulations run more stably?

Thanks in advance,
-Trayder

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