[gmx-users] fly some lipids to water

Justin A. Lemkul jalemkul at vt.edu
Mon May 14 20:28:46 CEST 2012

On 5/14/12 12:24 PM, Dariush Mohammadyani wrote:
> Dear Users,
> I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a box
> size 6*6*20 (nm^3). For making this system I used DOPC system with a zero
> surface tension and then I replaced each DOPC with one CL.
> Now, I got strange result, after long run, some of lipid (most of them are
> cardiolipin) fly away from bilayer and come inside the water.
> Does anybody know what is the problem? How should I fix my system?
> I am using Coarse grained model using MARTINI force field.

If you're sure this isn't a PBC artifact, it sounds like whatever parameters 
you're using are incorrect.  If they don't produce reasonable behavior, you need 
a better model.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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