[gmx-users] harmonic restraints

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 4 12:19:30 CET 2010

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.


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