[gmx-users] Reading XTC files from fortran90

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 1 22:20:07 CEST 2007

Hi Jones,

I'm not sure what you mean with "shape" and "that integer". There's
> > nothing much redundant in the .xtc file and there are no integers
> > having to do with box shape. In fact, there is no "shape"...
> Well, by "shape" I meant "cubic" and "truncated octahedral", for example.
> But the integer was my mistake (old dlpoly adaptions that just came to my
> mind, together with the first integer in the header of all xdrf files and
> that I could not find a proper meaning at time), thought for a moment that
> the first integer in the .xtc header mean the "shape of the box". Just
> played a bit later with the manual and recorded that it's only the 9 box
> parameters that are important to define that within gromacs. Sorry for that
> mistake.
I was sort of afraid you meant that. That's why I mentioned in my first mail
that there is no "shape". Cuboid or truncated octahedron (generalized) or
rhombic dodecahedron (generalized) are merely different representations of
the inifinite simulation system. The only thing you have there are the nine
numbers of the vectors defining the lattice. These are most naturally
represented by a triclinic box, but any periodic shape is possible, but only
useful for viewing purposes. Everything else is easier with three vectors...


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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