I'm performing a MD with a mixed lipid bilayer DPPC:DPPG (4:1). Using Charmm-gui I built a lipid bilayer constituted by 100 lipids. In pure lipid bilayer for example DPPC, I could compare area per lipid, thickness and deuterium order parameter. My doubt is which parameters do I have to monitor during the simulation. How can I see if this bilayer were stabilized? Does anyone have experience in this kind of situation?
Can you check what is the typical timing for equilibration of lipids in this type of simulation? What temprrature are you studying? These are gel phase lipids at room to body temperature so my guess is that the system will be even slower to equilibrate.
Thank you Stéphane for those papers. My interest is put together one small positive charged peptide to interact with the lipid bilayer.
Marité, I'm performing the MD simulations above the transition temperature, I don't have the exactly temperature value here. Actually I also think it'll be slower to equilibrate. When I performed MD from pure DPPG bilayer, it took about 100 ns to reach steady state. The system has 128 lipids.
Dear Danilo,
That is a problem that we faced when we studied binary bilayers.
To determine if your system is or not equilibrated, I recomend you that track the surface area per lipid or the order parameters of the mix bilayer, to determine that the system achieved an equilibrated state.
However, and in a first instance, you shoud study each of these lipids independiently previously to put both of them together, to warranty that everything is OK.
Unfortunatelly, thist is all what can be done.
Finally, I recommend you the reading of any of my papers related to this subject.
Regards
Javier
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