retaining antiparallel beta sheet
Posted: 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
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