[gmx-users] cholesterol bond rotation

Michael Weiner mdw224 at cornell.edu
Wed Jun 25 17:55:40 CEST 2014

I've built a lipid bilayer in Martini consisting of DPPC, DUPC, and cholesterol.  When I try to do an energy minimization using the minimization.mdp provided in the Martini lipid bilayer tutorial (http://md.chem.rug.nl/cgmartini/index.php/bilayers), I get a large number (several dozen) of LINCS warnings.  The warnings say that the bonds rotated more than 30 degrees.  In each case, the two beads forming the bond are in a cholesterol molecule.  When I look at the trajectory animation, I can see that these beads begin jiggling during the simulation, but there is no major change in the conformation of any cholesterol molecule.  Should I be concerned, or would it be safe to ignore these warnings?  
Thanks for any advice.  

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