[gmx-users] Fluctuations in HII phase

[Justin Lemkul]

On 5/3/18 10:36 PM, Mohsen Ramezanpour wrote:
> Hi Gromacs users,
>
> I have a cylinder composed of lipids with waters inside (HII phase).
> This lipid tube fluctuates along the Z-axis.
> That being said, if we slice the cylinder in the Z direction, the center of
> mass (COM) for each slice is moving around in the XY plane. You can imagine
> it as a 1D undulations in the Z direction.
>
> I want to quantitively show that some of these cylinders are more dynamics
> than others in nature.
>
> Snapshots from the system are one of the solutions but can not be used for
> quantitative comparisons between several systems with a different level of
> undulations. It just shows these systems are bent.
>
> The average size of the system in the Z direction and its fluctuations
> might be another naive quantity to be considered. If the Z size is fixed
> and the system is behaving like a wave, this would not give what I want
> either.
>
> So, I would like to know your opinion on what would be the best way to show
> such undulations in a quantitative way?

I would plot the x-y COM position as a function of some selection of 
atoms along z, and calculate the fluctuation in COM position about the 
mean. If the structure is indeed more dynamic, that slice should 
fluctuate more than another system that is more rigid. Think of it as 
the RMSF of the COM in the plane.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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