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
A
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
the
distances, or indeed the atom trajectories? Is it worth looking at the
velocity autocorrelations or is this a slightly different question?
Many thanks,
Anna
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