Sérgio,
A few minor questions:
1. is your system restrained at all?
2. after the MD are you doing any post-processing to your trajectory BEFORE
doing gist:
-- Are you aligning your trajectory to a structure or residues (RMS)?
-- Are you imaging your trajectory?
Thanks,
Jonathan
On Thu, Oct 20, 2016 at 11:38 AM, Sérgio Marques <smar96.gmail.com> wrote:
> 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 - 09:00:04 PDT
