Re: secondary structure restraints in coarse grain

From: Aron Broom (
Date: Tue Jul 24 2012 - 15:37:54 CDT

The MARTINI CG model used by NAMD is already secondary structure
constrained. That is, you give it the secondary structure of your protein,
and the dihedrals for the CG beads are locked into that kind of secondary
structure. But maybe you want something more than that?

On Tue, Jul 24, 2012 at 2:35 PM, Eun Kim <> wrote:

> Hello,
> I would greatly appreciate if anyone could help me on finding restraining
> the secondary structure of CG model.
> this constraints would be not on the space, but constraints on extra
> bonds.
> I find that there is a plugin/scripts for allatom models which generates
> extra bonds to be constrained, but not for the CG one.
> Any help please!
> Thanks in advance
> Eun

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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