<html><body bgcolor="#FFFFFF"><div><br></div><div>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. </div><div><br></div><div>Regular bonds are generally used!</div><div><br><br>On Mar 4, 2010, at 6:15, Ajeeta kaushiki <<a href="mailto:ajeetakaushiki@gmail.com">ajeetakaushiki@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>Dear Sir <br><div class="gmail_quote"><br>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 .<br> <br><br>Thanks & Regards <br><font color="#888888">Ajeeta <br>
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