[gmx-users] maining helix conformation

[Justin Lemkul]

On 6/7/13 8:43 PM, Sanku M wrote:
> Hi,
>    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.

Either should work.  Method 2 may be slightly more direct and less error-prone 
since the restraints can be easily written using genrestr.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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