[gmx-users] about box size (II)

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Sep 25 10:12:22 CEST 2006

Hi zzhwise1,

What about using a box that will actually fit your system, i.e. 3, 2,
6? Sounds rather intuitive to me. Also, the observation that your
system "inverts" has to do with periodic boundary conditions, i.c.
having the system centered at one of the box faces. There was a post
about this a few days ago. Nothing to worry about (think periodically,
or infinitely even).


On 9/23/06, zzhwise1 <zzhwise1 at 163.com> wrote:
> thanks chris.neale!
>  when i change  the size to 6.0 (my  system is 3,2,6)
> ,the upper monolayer turn around ,the bottom to the top ,top to  the bottom
> ,is it the too big size in the x and y direction? should i to enlarge my
> sysytem to (6,6,6) to suit the box size?
>   thanks!
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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