Hi Dan,
What you say makes sense! But in my case the edges of the gist box are
still far from the PBC border. However, the truth is that those very high
values of energy are always near the edges of the box...
But thanks for your comment!
************************************************
Sérgio Marques, PhD
Marie Curie Fellow at:
*Loschmidt Laboratories*
Department of Experimental Biology
Faculty of Science, Masaryk University
Kamenice 5/A13, 625 00 Brno, Czech Republic
Web: http://smarques.weebly.com/
On 20 October 2016 at 15:33, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Oct 19, 2016 at 4:56 PM, Steven Ramsey <vpsramsey.gmail.com>
> 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,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Thu Oct 20 2016 - 09:00:03 PDT
