[gmx-users] maining helix conformation

Sanku M msanku65 at yahoo.com
Sat Jun 8 02:43:16 CEST 2013

  I have a pair of polypeptides which are generated as ideal helix. I want to carry out their assembly/dis-assembly simulation by maintaining the helicity of them.
I wonder which of the methods for retaining helicity is better :
1. use a harmonic restraints using [bonds] directive using type 6  among the backbone amide Hbond between i and i+4th residue.
2. Use dihedral restraint to maintain phi and Psi.
Any help will be appreciated. 

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