Hi,
On Fri, Jun 22, 2012 at 11:07 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> As stated in the AmberTools 1.5 manual, cpptraj by default applies the
> 'image' procedure before calculating the distance. In my case, the two
> atoms in question definitely did not move out of the primary box,
The manual is a little misleading on this point. It is more accurate
to say that "the minimum-image convention is used", i.e. the shortest
distance is always used by default unless 'noimage' is specified.
> because they were fixed. Hence, the result should not change with or
> without the 'image' procedure.
Not so - if the two atoms A and B are on opposite sides of a
rectangular box for example, the minimum distance between the two will
not be across the box, but between A and the image of B (or vice
versa). I suspect this is what's happening in your case.
For peace of mind, if you could repeat the calc with either AT12
cpptraj or any version of ptraj that could help narrow things down. If
those numbers do not match then I would suspect a bug.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jun 22 2012 - 08:30:03 PDT
