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
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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