AMBER Archive (2006)

Subject: Re: AMBER: grid output

From: Sergey Samsonov (
Date: Tue Nov 07 2006 - 02:35:28 CST

Thank you very much for the help and the reference! Now it's more clear
how one
can interpret the results from grid command.

If I correctly understood from the article, the moment when 'the density
is seen' is quite arbitrary
but since one compares different site of the same simulation (or the
equivalent simulations) what one
should care is just relative values.


Thomas Cheatham wrote:
>> 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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