Re: [AMBER] Negative values in RDF analyses?

From: Daniel Roe <>
Date: Thu, 10 Dec 2020 06:07:46 -0500


I’ll need some more information. It’s not really possible for there to be
negative values in the histogram during trajectory processing, so the issue
must happen during normalization. Off the top of my head the only thing I
can think of is the masks have a lot of atoms in common, but I’m only
speculating. Can you provide the exact commands you gave cpptraj, and the
output, particularly any warnings or errors? Also if possible send the
topology and a corresponding frame to me off list so I can try to
reproduce. Thanks!


On Wed, Dec 9, 2020 at 8:45 AM Gustaf Olsson <> wrote:

> I am seeing negative values above some distance for some analyses
> []
> Analyses are run specifying residues as solvent/solute masks (:XXX)
> without atom detail.
> This seems to happen in larger systems with a high number of solvent and
> solute. In the left figure, say 200 solutes and 30000 water (a number of
> other molecules are included in the system making water:non-water about
> 50/50 by volume). In the right figure, results are from a simulated
> titration. The functions dropping to negative values at the shortest
> distances represent those with the highest number of “solute” molecules,
> 50 larger structures. Functions then dropp below zero at longer distances
> as the number of solute molecules are decreased. The four functions not
> dropping at all are those with the lowest number of "solute” molecules, 5.
> Is this a problem based on values calculated producing some strange
> behaviour or is this a problem with imaging and analyses? The graphs are
> from the same series of simulations and there is a big size difference
> between the solute analysed to the left and the one to the right, yet both
> display seemingly similar behaviour.
> Any suggestions/input would be appreciated
> Best regards
> // Gustaf
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Received on Thu Dec 10 2020 - 03:30:02 PST
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