From: Phelan Jr., Frederick R. Dr. (
Date: Mon Feb 23 2015 - 15:31:03 CST


I have an atomistic system consisting of water, ions, surfactants, and a carbon nanotube. The surfactants assemble on the tube forming a complex. I would like to compute the RDF of the water wrt to the surfactants on the surface of the tube.

The computation was done in LAMMPS. So, I created psf of the system using "topo readlammpsdata full"; closed; read in the trajectory; read in the psf; and I am able to compute the rdf of just the hydrogen and oxygen in the water using "name 12" and "name 14" as the "selection 1" and "selection 2" entries, and it looks like what you would expect. So, I am confident I have that much correct.

My question then is, how do I compute the rdf of the water molecules with respect to anything else? I am talking about VMD nomenclature here. I see that the individual molecules are showing up as residues. The water is essentially residue 101 thru 10,100. But, I think what I need something akin to the residuetype which in this case, unfortunately, has the value "nothing".

Many thanks,

Frederick R. Phelan Jr., Ph.D.
Polymers & Complex Fluids Group
Materials Science and Engineering Division
National Institute of Standards and Technology
100 Bureau Dr., STOP 8542
Gaithersburg, MD 20899-8542
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