[gmx-users] Increasing sigma

Justin Lemkul jalemkul at vt.edu
Sat May 6 00:52:22 CEST 2017

On 5/5/17 10:04 AM, Hannes Loeffler wrote:
> On Fri, 5 May 2017 15:09:09 +0200
> Pallavi Banerjee <pallavisept at students.iiserpune.ac.in> wrote:
>> I intend to perform thermodynamic integration of my system, but not to
>> calculate the free energy. I want to gradually increase the radius of
>> the carbon atoms of the alkyl chains of my lipid molecules. This is
>> because I could see a hole forming in my lipid bilayer along the
>> edges of the simulation box and the water molecules pass through it.
>> Once the system with the bigger radius equilibrates, I would then
>> gradually beat down the radius to the original value.
> I don't think that would solve your problem.  You would be pretending
> that your lipids (and thus the box size) are larger then they are but
> what the bilayer really wants to do is to contract.  And water is very
> quick in filling the voids.  So if you decrease the radii again you may
> just be back where you have started because your lipids still need to
> attain the desired density.

I agree.  The better approach is to apply a mild restraint along z to all water 
oxygen atoms and equilibrate.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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