[gmx-users] question about non-orthongonal box vectors in pdc

Michael Shirts mrshirts at gmail.com
Thu Mar 30 07:00:49 CEST 2006

So, to get a truncated octahedron, or some other shape, you use
certain ratios for the box vectors as detailed in the manual.  But the
box vectors in the .gro file are truncated to a certain precision, so
don't exactly meet these ratios.  What is the consequence of not
exactly meeting these ratios?  It won't precisely fill space in a
periodic way -- so does it mess up the pbc in some way?  Anyone know? 
 Any experiences?  Should I make sure the ratios are correct up to
machine precision?  Is there a way to handle this more robustly?

Michael Shirts
Research Fellow
Columbia University

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