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

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 20:07:53 CET 2013

On 1/10/13 10:07 AM, Anna Duncan wrote:
> 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?

I don't understand why you would smooth the data.  From the description, it 
seems like you are trying to determine the length of time that the lipid is 
within a certain distance of the protein as a measure of its interaction.  The 
raw data should be sufficient to accomplish that.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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