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

Michael Shirts mrshirts at gmail.com
Thu Mar 30 07:01:37 CEST 2006

That would be pbc (periodic boundary conditions), not pdc (who knows
what that is), of course . . .

On 3/30/06, Michael Shirts <mrshirts at gmail.com> wrote:
> 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?
> Thanks,
> Michael Shirts
> Research Fellow
> Columbia University

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