AMBER Archive (2006)

Subject: Re: AMBER: grid output

From: Thomas Cheatham (
Date: Mon Nov 06 2006 - 22:30:25 CST

> I've been using grid command for water molecules in ptraj AMBER module and
> visualising the results in vmd (selecting Xplor file format for the grid
> output).
> Does anybody know in which units the isovalues are expressed in this case? I
> wonder if this command could be used for some quantitative estimations of
> density
> distribution or it is just useful to obtain the results to visualize the
> density (and the isovalues don't have really important meaning).

The "grid" density is simply the count of the selected atoms over the
trajectory in each grid element and therefore can be directly compared to
expected counts (i.e. given a known density) per grid element. This was
discussed briefly in the methods to JACS 119, 4805-4825 (1997) where for
1000 frames and a (0.5 A)**3 grid, water oxygens have the expected density
of 4.18. Normally, I contour at 2-3x bulk (water) density. The
conversion will obviously change as a function of the grid size and number
of frames.

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