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
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 24 2016 - 00:30:02 PDT
