On 7/16/13 3:43 PM, Dariush Mohammadyani wrote:
Dear All,
I have set two bilayers:
1. 400 DOPC
2. 320DOPC and 80 Cardiolipin
Second one show significant curvature during NPT equilibrium and MD run
(not in NVT eq.). Is it normal?
You could be undergoing some sort of phase transition, but in the absence of a
lot more information, it's hard to say. Pronounced curvature of a small patch
of lipids sounds odd.
For the first bilayer, after adding the protein to the system, here also I
can see big curvature in the membrane.
Some proteins induce membrane curvature, but I suspect if you were working with
one of those, you'd know that curvature is normal in those cases :) Hydrophobic
mismatch can play a role in perturbing lipid dynamics.
Does anybody knows is it normal or something is wrong?
Which factors do affect the membrane curvature (like: initial conf., water,
ions, box size, equilibration steps, ...)?
Force field, temperature, .mdp settings, you name it - membranes can be very
finicky. It would help to have:
1. Links to where you have posted illustrative images
2. What force field you're using and your .mdp
3. What protein you're working with (if you can say)
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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