Membrane Simulation

From: Alice Zheng (zheng53_at_uic.edu)
Date: Tue Oct 30 2018 - 20:58:03 CDT

Dear all,

I am trying to simulate a membrane bilayer on top of water. In the
experiment, there is helium gas on top of the bilayer. If I use PME with
periodic boundary conditions, I have to leave vacuum on top of water. When
I use NVT for a larger system, the membrane becomes corrugated due to the
lack of a surface tension force applied to the membrane. Changing
SurfaceTensionTarget does not prevent the membrane from being corrugated.

Is there a way to apply a surface tension force while using NVT? Or is
there a way to use NPT for the system? Are there other ensembles that are
appropriate for this type of system with bilayer lipid membrane situated
between a aqueous and a gas phase?

I also tried using MSM and tried to eliminate the periodicity in the z
direction (perpendicular to the membrane). However, I ended up with an
error message saying that a atom is outside the MSM grid when I did energy
minimization. The periodicity in x and y could also not be displayed in VMD.

Is it possible to have only 2D periodicity using PME? (Whenever I commented
out cellBasisVector3, I ended up with the error message that "PME requires
boundary conditions.")

Any help would be greatly appreciated.

Thank you,
Alice

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