Imaging is done via fractional coordinates in sander and pmemd; I believe it
to be okay. I noticed a simple distance calculation in shake a while back,
but there you are dealing with bonded atoms at real coordinates.
Regards - Bob Duke
----- Original Message -----
From: "Jun Wang" <jwang20.uci.edu>
To: <amber-developers.scripps.edu>
Sent: Monday, September 17, 2007 9:46 PM
Subject: amber-developers: About calculating the minimum imaged distance
> The program ptraj may give out the incorrect minimum imaged distance
> between two atoms when the non-imaged distance between the atoms is
> greater than two times the box size. This is caused by the function
> calculateDistance2. I am not sure whether the programs sander and pmemd
> have the same bug. Can someone give me the answer of this question?
>
> ===========================================
> Jun Wang, Ph.D.
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> Phone: (949) 824-9562
> Email: jwang20.uci.edu
> ===========================================
>
>
Received on Wed Sep 19 2007 - 06:07:29 PDT
