From: Axel Kohlmeyer (
Date: Sat Mar 17 2007 - 15:48:44 CDT

On Sat, 17 Mar 2007, lanhua wrote:

L> Hi,

L> I am new to VMD. I installed VMD in windows and I wanna calculate
L> the oxygen-oxygen radial distribution function of water which are 15
L> angstrom away from protein and such water I think could be pure
L> water. So I did the calculation in the window of Radial Pair
L> Distribution Function g(r), and the input parameters are:

L> Selection 1: (water not within 15 of protein) and name OH2
L> Selection 2: (water not within 15 of protein) and name OH2
L> Frames: First: 0 Last: 199 Step: 2
L> Histogram Parameters: delta r: 0.1 max r: 20
L> Use PBC (Yes) Update Selections (Yes) Display g(r) (Yes)

L> The size of my simulation box is 78*78*78.

L> But I can't get the same pair distribution function as pure water and
L> g(r) I got can't reach 1 even at 20 angstrom. I hope someone can tell
L> me how to fix this problem and what kind of sample scripts I can use
L> to calculate the radial pair distribution function of water around
L> some protein surface atom in VMD.

your g(r) will never reach 1 because you do not have a homogeneous
density in your selection. whenever you are 'sitting' on a water,
you'll have a higher number density of water molecules in the
neighborhood, than the total numberdensity averaged over the
whole box. the 'vacuum' will always be far away. you have to
think very carefully about what will be the right normalization
and how to properly compute the g(r) in a way that it would
reproduce the bulk water case (in fact, you'd have to do a
different normalization for each water).

of course a generic tool like the g(r) plugin cannot do this.
regardless, the peak _positions_ should be correct. there is
very little structure in water beyond r=15 angstrom, so there
is little point discussing about whether you reach 1 or not.


L> Thanks
L> Lan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.