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/
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--
-------------------------
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 Thu Mar 30 2017 - 05:30:06 PDT
