[gmx-users] cholesterol bond rotation

Michael Weiner mdw224 at cornell.edu
Thu Jun 26 20:52:41 CEST 2014

Thanks, Justin.  
I tried the minimization with just a lone cholesterol molecule, and there were no LINCS warnings.  Additionally, I tried a production run on the full system, and it didn't seem to encounter any further issues.  I suspect that you are right in suggesting that the initial configuration is to blame.  

> Date: Wed, 25 Jun 2014 17:35:49 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cholesterol bond rotation
> Message-ID: <53AB40B5.1060002 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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
> -- 
> ==================================================
> 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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