[gmx-users] box curiosity

Ken Rotondi ksr at chemistry.umass.edu
Thu Aug 4 18:13:02 CEST 2005

Hi all,

I'm running an NVT simulation with a box-size of 75Å cubed (-box 7.5 
7.5 7.5) I've done a gmxdump on my output files (.trr & .xtc). I was 
surprised to find this in the output:

    box (3x3):
       box[    0]={ 7.50000e+00,  0.00000e+00,  0.00000e+00}
       box[    1]={ 0.00000e+00,  7.50000e+00,  0.00000e+00}
       box[    2]={ 3.75000e+00,  3.75000e+00,  5.30330e+00}

I would think that this represents the X,Y,Z dimensions of the box, so 
box 0 and 1 make sense, but I don't understand the box 2 output. Can 
anyone give me insight?



K.S. Rotondi Ph.D.
Research Fellow
The Gierasch Laboratory
Department of Biochemistry and Molecular Biology
University of Massachusetts-Amherst
Phone: 413-545-1250
Fax;      413-545-3291
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