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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Received on Wed Mar 29 2017 - 19:30:02 PDT
