Hi Jonathan,
My system has no restraints. I always center, align and image my systems
before analyzing them. For this one in particular, I also removed the ions.
Regards,
Sergio
************************************************
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 17:51, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> 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 Fri Oct 21 2016 - 04:30:03 PDT
