Re: [AMBER] about grid & radial distribution function

From: Thomas Cheatham <>
Date: Thu, 29 Jul 2010 20:03:07 -0600 (Mountain Daylight Time)

> #1: I have problem in adjusting the amount of *spacing* in *grid* and
> also *radial
> distribution function* in ptraj.
> Are they arbitrary values or should be calculated according a reference?

Yes, arbitrary, but certain values make more sense than others. I tend to
use 0.5 A spacing and a 100 grid (50 A). RDF similar.

> #2: Is it necessary to center and image (solute and solvent) prior to the *
> radial* call?

Yes, most definitely. For the radial, this is not necessary since imaging
is implicitly done. However, for the grid you want the "solute" in a
common reference frame with all nearby water around it (and not in
periodic frames),


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Received on Thu Jul 29 2010 - 19:30:03 PDT
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