From: Axel Kohlmeyer (
Date: Thu Dec 30 2010 - 14:53:56 CST

On Wed, Dec 29, 2010 at 6:57 PM, Xijun Wang <> wrote:
> Hello,
> Would someone give me some hints to generate the angular or spatial
> correlation function with VolMap tool?
> I want to generate a probability density map: the probability of
> finding the solvent molecule around a solute molecules. It is called
> "atomic density map" in literature such as JACS, 126, 11462(2004).
> They were generated by the Volmap Tool of VMD. But after carefully
> reading the manual/tutorial and seraching in the mail-list, I still do
> not know how to do that. In the GUI of VolMap, there is only one place
> to input the "selection", for example, to input "water and name OH2"
> as a selection, but how can I input the selection of  solute molecule?

you don't have to.
all you have to do is to first align the trajectory, so that
your reference solute molecules are all on top of each
other throughout the trajectory. then all you have to do is
to compute the density map for the solvent.

this becomes more complex, if you have multiple solute
molecules. then you have to do multiple volmap runs
(please keep in mind that the GUI is just a frontend for
the script command, so you can automate the process)
and then write a small tool to average over the resulting
grid files.

> Any suggestion is appreciated.
> Xijun Wang
> --
> Department of Chemistry and Biochemistry
> Concordia University
> 7141 Sherbrooke West, Montreal, Quebec H4B 1R6

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.