[gmx-users] Fluctuations in HII phase

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Fri May 4 04:36:17 CEST 2018

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

So, I would like to know your opinion on what would be the best way to show
such undulations in a quantitative way?

Thanks in advance for your comments.

*Rewards work better than punishment ...*

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