[gmx-users] PBC problem

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 16 06:48:46 CEST 2007

Hi Yuguang,

> Warning: Triclinic box is too skewed.
>          Box (3x3):
>             Box[    0]={ 6.46530e+00,  0.00000e+00,  0.00000e+00}
>             Box[    1]={ 2.14552e+00,  6.10274e+00,  0.00000e+00}
>             Box[    2]={-2.14464e+00,  3.05200e+00,  5.24664e+00}

This is not a rhombic dodecahedron.

> CRYST1   64.653   64.689   64.375  70.32 109.46  70.63 P 1           1

This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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