[gmx-users] Re: How to choose appropriate size for a sliding average for smoothing distances between molecule types

[anna.duncan]

Thank you for your reply. 

You're right that I want to measure the protein-lipid interaction by
determining the length of time that the lipid is within a certain distance
of the protein.  However,  I also want to get a measure of the length of
time that the lipid is continuously interacting with the protein, that is,
whether a given lipid has lots of short periods of interaction with the
protein or just one fairly long interaction time.

For this purpose, the small fluctuations (what you might call thermal
noise?) in the positions of, and distances between, a given lipid and the
protein mean that using the raw data gives lots of short interaction times,
whereas the global motion of the given lipid in relation to the protein may
be very little.  I've attached an image that will hopefully make this
clearer.  The image shows the minimum distance between a given lipid
particle and the protein molecule over the course of the simulation.

I am performing coarse-grained simulations, using MARTINI, so the
fluctuations in position (and thus inter-particle distance) will be greater
in magnitude than for atomistic simulations, I would have thought, seeing as
the timestep is larger.  This may mean that the problem is more (or only)
pertinent for coarse-grained simulations, although I'm not sure about this.  

<http://gromacs.5086.n6.nabble.com/file/n5004497/distance_thermal_noise_example2.jpg> 



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