retaining antiparallel beta sheet

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Daniel Konstantinovsky
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retaining antiparallel beta sheet

Post by Daniel Konstantinovsky » Mon Feb 28, 2022 10:58 am

Hi OpenMM!

I am simulating an antiparallel beta sheet that likes to fall apart during equilibration. I need to prevent this. I am wondering if anyone on this forum has any advice for keeping the beta sheet together. I was thinking to use CustomNonbondedForce between a few particular atoms in the adjacent strands to keep them together. Do you recommend a flat bottom or harmonic potential? What other advice do you have for someone trying to do this? I realize what I'm simulating is somewhat artificial but that's fine for my purposes right now. Please advise anything you can think of!

Thank you!
Dan
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Peter Eastman
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Re: retaining antiparallel beta sheet

Post by Peter Eastman » Mon Feb 28, 2022 12:02 pm

If you want a constraint between a few specific atoms, you probably want a CustomBondForce, not CustomNonbonedForce. As for questions about potential shape, strength, etc. I'll leave that to people with more experience doing that sort of thing.
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Daniel Konstantinovsky
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Re: retaining antiparallel beta sheet

Post by Daniel Konstantinovsky » Mon Feb 28, 2022 1:18 pm

Oh ok, thank you, I will use a bond force.
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