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.

Regards,
Kevin

*----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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