Hello everyone, I am trying to simulate an Alpha helix inside a bilayer. But a part of the alpha helix is loosing its form and converting into turns( while alphahelix should be stable in the bilayer environment) I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. I am using Potential-switch for VdW and PME for electrostatics. Does these parameters affect the form of the Alphahelix ?
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