VMD-L Mailing List

From: Narayanan Veeraraghavan (narayanan.veeraraghavan_at_gmail.com)
Date: Wed Jan 26 2011 - 17:30:33 CST

Hi,
I am using the g(r) gui to calculate the g(r) of solvent metal ions, say,
Na+ around three specific atoms of my protein (different atom types,
belonging to different residues but close to each other in space).

Now, my question is, how is the r determined? Is it from the *geometric
center* of three atoms? Or, does it select all Na+ atoms within r of
*atleast one* of the three atoms? Or does the function do some kind of
averaging of the g(r) from each of these three atoms? Would appreciate
specific pointers.

Details:
selection1: index 10 35 1090
selection 2: resname NA
Assume some values for delta and max r.

Thanks,
Narayanan