Re: Bubble in water during membrane simulations

From: Giacomo Fiorin (
Date: Mon Nov 16 2015 - 09:48:42 CST

Hello Kevin, if you replicated a model membrane once in either the x or y
direction along its periodicity vector, it should be fine. That, or you
can supply specific x and y dimensions to C-GUI.

There isn't much information about the source of error, but a general
recommendation for membrane models is to generate tiny ones, equilibrate
them, and then replicate them as needed. This would save both CPU hours
(small membranes can be simulated very cheaply)
and simulation time (oscillations of small membranes have fast time scales,
and will equilibrate sooner).

On Mon, Nov 16, 2015 at 3:12 AM, Kevin C Chan <>

> 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
> <>*

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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