From: lanhua (
Date: Sat Mar 17 2007 - 14:30:31 CDT

    I am new to VMD. I installed VMD in windows and I wanna calculate the oxygen-oxygen radial distribution function of water which are 15 angstrom away from protein and such water I think could be pure water. So I did the calculation in the window of Radial Pair Distribution Function g(r), and the input parameters are:
    Selection 1: (water not within 15 of protein) and name OH2
    Selection 2: (water not within 15 of protein) and name OH2
    Frames: First: 0 Last: 199 Step: 2
    Histogram Parameters: delta r: 0.1 max r: 20
     Use PBC (Yes) Update Selections (Yes) Display g(r) (Yes)

The size of my simulation box is 78*78*78.
But I can't get the same pair distribution function as pure water and g(r) I got can't reach 1 even at 20 angstrom. I hope someone can tell me how to fix this problem and what kind of sample scripts I can use to calculate the radial pair distribution function of water around some protein surface atom in VMD.