[gmx-users] Unstable Alpha Helix

[amitbehra at chemeng.iisc.ernet.in]

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 ?

Regards,
Amit

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