[gmx-users] harmonic restraints

[Mark Abraham]

On 4/03/2010 10:15 PM, Ajeeta kaushiki wrote:
> Dear Sir
>
> I am doing a coarse grain MD of a membrane protein using Martini force
> field and parameters  . In course I am facing problem in understanding "
> how the harmonic restraints will be applied to mimic secondary structure
> H- Bonds of the atomic structure to the coarse grain model to maintain
> secondary structure element " . Is this will be specified in the 'mdp'
> file .

These might be applied in various ways - see chapters 4 and 5 of the 
manual for some discussion.

Mark