unanswered Dealing with amide rotation

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1 year 1 month ago #9612 by mdsimulationgroup
Dealing with amide rotation was created by mdsimulationgroup
Hello,

I'm working on a structure that has an amide. Due to cis/trans states of the amide, I'm getting some "complex" bond and angle distributions. I'm mapping the CG bead at the center of C-N bond. I could do a few things to deal with the bond/angle distributions: 1) only use one fixed state cis or trans, 2) use an averaged potential, 3) use a polynomial fit to conserve state information. My question, what is typically done to handle amides?

Thanks,
Frank

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