Thanks, Dan! I'll give this a try. Appreciate it.
Joe
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
On Thu, Mar 30, 2017 at 8:20 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> In the GitHub version of cpptraj (https://github.com/Amber-MD/cpptraj)
> you can specify part of a molecule as the anchor instead of the entire
> molecule. I've found that this usually fixes imaging issues. Just pick
> a residue in your molecule that you would like at the center of the
> unit cell, e.g.:
>
> autoimage anchor :23
>
> Hope this helps,
>
> -Dan
>
> On Wed, Mar 29, 2017 at 10:10 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> > Hi all,
> >
> > A student of mine has run a simulation of a protein filament (18
> subunits),
> > and the filament tilts a bit in the water box after several hundred
> > nanoseconds of simulation, at which point a monomer at the end of the
> > filament "appears" on the other face of the periodic box. During the
> > simulation I am using iwrap=1.
> >
> > To remedy this we have tried using autoimage in cpptraj leaving the
> anchor
> > molecule as the default molecule (and have tried a few of the other
> > monomers as the anchor as well), but have not been able to successfully
> > reconstruct the filament trajectory without the artificial jumps in the
> > coordinates of some monomer(s) (depending on the choice of anchor
> molecule).
> >
> > This doesn't impact calculations internal to an individual monomer (RMSD,
> > distances, etc), but impacts calculation of the overall filament backbone
> > RMSD for example.
> >
> > Are there any suggestions about how to go about addressing this?
> >
> > Thanks for any help.
> >
> > Joe
> >
> > ------
> > Joseph Baker, PhD
> > Assistant Professor
> > Department of Chemistry
> > C101 Science Complex
> > The College of New Jersey
> > Ewing, NJ 08628
> > Web: http://bakerj.pages.tcnj.edu/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Thu Mar 30 2017 - 11:00:03 PDT
