[AMBER] "image" command with "familiar" option

From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Thu, 9 Jan 2014 18:03:13 +0900

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.

It might be less important question but
I am most grateful if you give me a reply.

Yours sincerely,

                                            Ikuo KURISAKI

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Received on Thu Jan 09 2014 - 01:30:03 PST
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