Unfortunately, That explains your weird results. You can trust the density
and maybe a some of the other things, but the energy is going to be
significantly off.
One alternative is to look at the rmsf of the backbone and look for atoms
that don't move. You could then re-run the MD keeping a few points fixed
with loose restraints. That would keep the system in one place, then run
gist. there will be no need for alignment as it will be stuck in one
position.
Hope that helps.
On Fri, Oct 21, 2016 at 7:13 AM, Sérgio Marques <smar96.gmail.com> wrote:
> 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 - 11:30:02 PDT
