Re: [AMBER] Help with GIST analysis

From: Daniel Roe <>
Date: Thu, 20 Oct 2016 09:33:10 -0400


On Wed, Oct 19, 2016 at 4:56 PM, Steven Ramsey <> wrote:
> There is a known issue when applying GIST to unrestrained systems that are
> then aligned using rms in cpptraj that produces arbitrarily high energies
> and that sounds to be the issue at hand with your Eww being 1.12E+06. If
> possible you may want to avoid aligning the system prior to running GIST.

Just to expand on this a bit, this is an unavoidable consequence of
using periodic boundary conditions. By default, GIST will use the
minimum imaged distance between particles when performing the
non-bonded energy calculation for trajectories containing unit cell
information. If you perform a system alignment prior to GIST (or
really any analysis that performs imaging), the system will no longer
be aligned with the original unit cell, which usually leads to clashes
between particles and imaged particles and hence the high energies.
You can easily illustrate this in 2 dimensions with two pieces of
paper (the paper being your unit cell). You can lay the papers side by
side so that the edges align perfectly. However, if you then rotate
both pieces of paper by 45 degrees clockwise the papers will overlap,
and any "particles" in that overlapping region will probably clash.

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu Oct 20 2016 - 07:00:02 PDT
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