VMD-L Mailing List

From: Paymon Pirzadeh (ppirzade_at_ucalgary.ca)
Date: Mon Feb 13 2012 - 15:21:25 CST

Hello,
I am trying to calculate the radial distribution of water molecules with
respect to a few surface residues of my protein. The final profile
clearly is not properly normalized since apparently the module does not
care about the empty volume portion properly. The profile starts from
some values close to zero, with a peak at 1.75A (consistent with
literature) and increases up to some number but not 1 in long distances.
I have removed pbc and I am updating the selection (along the
trajectory). Can anyone tell me how I can properly normalize this
function?
Best,

Paymon