[gmx-developers] helix constraint

[Gerrit Groenhof]

Hi Lakshmi,

>                 i would like to do MD simulations of a protein which is 
> unfolded manually. when i do the MD simulations the secondary structure 
> (HELIX) should be constrained. only helices should constrained or restrained,
> how can i do it?
> 
> is it possible to make this in gromacs? I hope some one of you could help me.

Maybe you can simply put distance restraints on the hydrogen bonds
that are needed to keep the alpha helix in shape. Or define harmonic
bonds (bond type 6 I think) and put a constraint on them. It is only
the helices you want to constrain?

Good luck,

Gerrit