AMBER Archive (2008)

Subject: Re: AMBER: Leap atoms CL and OXT do not have a type

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 29 2008 - 17:03:28 CDT

> > I believe the first peak of the radial distribution in dynamics would be
> > the ideal measurement to consider.
>
> Could you please address me where to learn about, and, should you find
> the time, vulgarize a bit this last sentence?

You could read the paper I referenced:

    Ion-Induced Stabilization of the G-DNA Quadruplex:
    Free Energy Perturbation Studies. W.S. Ross and C.C. Hardin
    Journal of the American Chemical Society 116, 6070 (1994).

Radial distribution is represented by a graph of the density of one type
of atoms around another, where the x-axis is distance, averaged over all
cases of interest in a trajectory. The first peak represents the average
distance of the closest pair(s). Ptraj can calculate radial distribution.

Bill
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