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

Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk
Thu Jan 10 16:07:03 CET 2013

 I have performed a simulation of a protein in a lipid bilayer and I
 want to look at the lengths of time that a particular lipid type, lipid
 type A, say, remains within a certain distance of the protein.

 I have calculated the distances between lipid type A and the protein.
 Obviously, the trajectories of each particle are not smooth, so neither
 are the distances between atoms of lipid type A and the protein.
 Because I want to look at a continuous amounts of time that lipid type 
 molecules are proximal to the protein, it seems to make sense to smooth
 the distances, using xmgrace, for instance.  Does this make sense to
 you?  If so, how should I go about determining by how much to smooth 
 distances, or indeed the atom trajectories?  Is it worth looking at the
 velocity autocorrelations or is this a slightly different question?

 Many thanks,


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