From: 翁林岽 (wenglindong_at_yahoo.com.cn)
Date: Fri Jun 07 2013 - 20:36:44 CDT
When I equilibrate a DPPC/water system, the center of the lipid bilayer always shifts by several Ås along the Z axis. Since the center of the simulation box is kept at (0, 0, 0), the consequence is that 1) the water layer on one side is squeezed into the neighbor periodical box and gradually shrinks and 2) the water layer on the other side correspondingly becomes thicker due to the periodical conditions I think. As the equilibration goes on, the shrinking water layer becomes a very thin layer. Does anyone observe the same problem in your simulation?
I am afraid that the lipid bilayer may eventually be seperated by the periodical boundary so that the original water<--->lipid bilayer<--->water complex will become a lipid monolayer<--->water<--->lipid monolayer one in the simulation box. Probably, with periodical conditions, such changes will not negatively affect the simulation accuracy. But can anyone tell me why there is such shift? Are these changes normal or acceptable? Are there any ways we can avoid such shifts and make the simulation box look normal?
Any suggestions would be really appreciated.
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