Hi Sergio,
That's a nice way to use gistpp to eliminate high energy results.
Unfortunately removing these high energies from your analysis will not fix
the issue, all of the energetic values produced by GIST are performed using
a pairwise distance, when the system is realigned these distances are
compromised. Despite the other energies appearing to be normal it is hard
to have confidence in their accuracy. The best way to run GIST currently is
to use a restrained system as Jonathan suggested in the previous post. The
entropies you are calculating should work in a re-aligned system.
Hope this helps,
--Steve
On Mon, Oct 24, 2016 at 3:22 AM, Sérgio Marques <smar96.gmail.com> wrote:
> Hi Jonathan,
>
> I was thinking that maybe we might use gistpp to set up some cutoff for the
> energies per voxel, like -10 < Etot < 10 kcal/mol, so we could discard
> those points with obviously wrong values (e.g.: ./gistpp -i gist-Etot.dx
> -i2 gist-Etot.dx -op clear2 -opt cutoff1 -10.0 -opt gt1 -opt cutoff2 10
> -opt lt2 -o correctedEn.dx). Visualizing those few high energies regions,
> they always locate near the edges of the box, so in reality those points
> should not be affected by the residue that I'm focused on (in the center of
> the box).
> Do you think this wouldn't be enough to correct the miscalculations?
>
>
>
> ************************************************
> 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 21 October 2016 at 20:17, Jonathan Gough <jonathan.d.gough.gmail.com>
> wrote:
>
> > 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 Mon Oct 24 2016 - 10:30:03 PDT
