Hi,
All imaging routines ('autoimage', 'image') will correctly place atoms
inside a unit cell unless your box coordinates (used to create the
unit cell vectors) are not right for some reason, such as trying to
image after rms-fitting.
Without a better description or example of your problem with
'autoimage' I can't begin to help with that. However, I can tell you
that a 'center' command following an imaging command, e.g.:
> image center :1-77562 bymask familiar
> center :1-2
can definitely shift atoms outside the box - any action that modifies
coordinates after an imaging command can. Typically you center first,
then image (this is what 'autoimage' does internally). If you had a
'center' command following 'autoimage' this would do the same thing.
If you can give a more complete description of your issue I may be
able to help further.
-Dan
PS - As always, make sure you're using the latest version of cpptraj (14.09).
> image center :1-77562 bymask familiar
> center :2-3
> image center :1-77562 bymask familiar
> center :3-4
> image center :1-77562 bymask familiar
> center :1-5
> image center :1-77562 bymask familiar
> center :5-6
> image center :1-77562 bymask familiar
> center :6-7
> image center :1-77562 bymask familiar
> center :7-8
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Oct 29 2014 - 08:30:03 PDT
