Constraints required for alpha helix secondary structure

From: Diship Srivastava (
Date: Fri Jul 16 2021 - 05:51:56 CDT

I have protein containing 28 mino acid residues. The protein has 4 leucine
residues which forms 2 leucine zipper structures and whole protein adopting
alpha helix config with several salt bridges between different residues. I
started with a structure similar to this ( made by Avogadro) and I was able
to get proper psf file. During equilibration with protein in water box
whole protein loses its alpha helix config ( I measured the alpha helix
content using alpha helix colvar) resulting in an open ended structure with
less than 20% alpha helix content which was around 75 % in the initial

My question is what constraint do I apply to protein such that I get
accurate description of it during equilibration and production run? Also on
applying these constraints will it affect the PES of the system?

Diship Srivastava
IIT (ISM) Dhanbad

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