[gmx-users] Fluctuations in HII phase

[Mohsen Ramezanpour]

Thanks Justin! It sounds an interesting approach. I will give it a try.

Cheers,
Mohsen




On Fri, May 4, 2018 at 8:15 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
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> Virginia Tech Department of Biochemistry
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