[gmx-users] harmonic restraints

XAvier Periole x.periole at rug.nl
Thu Mar 4 15:28:06 CET 2010

It is not sure what you mean: if you wonder how it is done in Martini  
(explained in the paper) or if like to add some yourself.

Regular bonds are generally used!

On Mar 4, 2010, at 6:15, Ajeeta kaushiki <ajeetakaushiki at gmail.com>  

> 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 .
> Thanks & Regards
> Ajeeta
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