Dear Jason,
Thank you for your reply.
My question is solved.
Yours sincerely,
And a happy new year.
KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Friday, January 10, 2014 12:45 AM
To: amber.ambermd.org
Subject: Re: [AMBER] "image" command with "familiar" option
On Thu, 2014-01-09 at 18:03 +0900, kurisaki wrote:
> Dear Amber developer,
>
> I find that "image" command with "familiar" option are prepared for a
> system in truncated octahedral box.
> However, I cannot find any difference between with-"familiar"
> and without-"familiar" when I analyzed a system in rectangular box.
> (I am analyzing water molecules around protein, thus "image"
> should influence the following analysis.)
>
> Please assume that we analyze a system in rectanglar box.
> If we use "image" command with "familiar" option for the system, does
> it cause serious artifacts such like atomic crash of water surrounding
> protein, basically?
> Or does ptraj automatically neglect "familiar" option when it treat a
> system in rectangular box.
The answer is that a "familiar" representation of an orthorhombic box (with all
90-degree angles) is equivalent to standard, non-familiar imaging, so there
appears to be no difference.
All of the standard periodic shapes we use (orthorhombic, truncated octahedron,
rombic dodecahedron, etc.) can be rearranged as a general triclinic cell defined
by 3 vectors and the angles between them. The standard imaging approach
rebuilds this general triclinic cell, so any non-orthorhombic cell (like a
truncated octahedron) will look quite different than you would expect it to.
When you use the 'familiar'
keyword, cpptraj and ptraj will automatically take the most spherically
symmetric representation of that unit cell (i.e., they will take the image of
all atoms that are closest to a pre-defined 'origin'). When all angles are 90
degrees, the standard triclinic cell _is_ the most spherically symmetric
representation---this is why 'familiar' and non-'familiar' are equivalent in
this case.
HTH,
Jason
P.S. As an aside, cpptraj has a nifty "autoimage" command that will
automatically do the 'centering' and 'imaging' for you, invoking 'familiar' when
need be. It is quite helpful in cases like these.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 09 2014 - 17:00:07 PST
