[gmx-users] cholesterol bond rotation

[Justin Lemkul]

On 6/25/14, 11:55 AM, Michael Weiner wrote:
> Hello, 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?

During EM, these may not indicate a serious problem (bad clashes in the initial 
configuration can do that), but no sane dynamics simulation should produce LINCS 
warnings.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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