AMBER Archive (2006)

Subject: AMBER: "noimage" option for radial distribution functions

From: Ozlem Demir (
Date: Sun Jul 16 2006 - 16:14:31 CDT

Hi All,

I am preparing radial distribution function of water around the ligand during an
MD simulation of a protein. I have used iwrap=1 during MD and then used ptraj to
center. Should I use noimage option during radial distribution function
calculations? What does "noimage" option exactly do for r.d.f calculations? How
about for "closest" or "watershell" calculations in ptraj?

Best ,

Ozlem Demir

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