Bubble in water during membrane simulations

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Nov 16 2015 - 02:12:29 CST

Dear Users,

I am doing membrane simulations and I created bilayers from CHARMMGUI.
While I do some regular equilibrium protocols on simple membrane in water
simulations, I would find my water boxes shrink unusually much towards the
z-axis especially after graduate heating up (NVT) and did not recover even
after nanoseconds of some more NPT runs.

I understand that in sense of PBC, although it looks like my water box was
truncated at the eight corners, it actually represents a bubble inside
water. I have searched the list and Axel once mentioned this as "safety
bubble". Is it normal during the equilibrium of membrane-water simulations?
As I do have few cases that the water finally recover like nothing has
happened. So I just have to do more NPT runs until it looks normal?

One more thing, the situation happened when I simulated a rectangular
membrane composed by two square membranes generated from CHARMMGUI (simply
as CHARMMGUI does not provide rectangular shapes). Is it due to "badly"
piecing membranes together?

Thanks in advance.


*----PhD CandidateDepartment of Physics and Material ScienceCity University
of Hong Kongcchan2242-c_at_my.cityu.edu.hk <cchan2242-c_at_my.cityu.edu.hk>*

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