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

[Erik Lindahl]

Hi,

As Tsjerk wrote we always work with the triclinic representation in  
the code, which fills up space nicely. Due to rounding it might not  
be a _perfect_ representation of e.g. a hexagonal box, truncated  
octahedron, rhombic dodecahedron, etc., but that shouldn't affect the  
physics of the triclinic box.

The reason I first asked about boxes is that the PME grid too has to  
be triclinic for such boxes, and I don't think anybody has done any  
detail PME accuracy analysis in the case of severely skewed boxes.

Cheers,

Erik

On Mar 30, 2006, at 9:43 AM, Tsjerk Wassenaar wrote:

> Hi Michael,
>
> It will in any case still fill up space in a periodic way. That can  
> be done with an infinite number of triclinic boxes, of which the  
> formal (perfectly regular) truncated octahedron is only one.  
> Besides, the shift vectors are used to calculate the distances  
> between particles, determine the neighbour lists, etc. If the  
> coordinates are only stored with a certain precision, there is no  
> point in having lattice vectors (box vectors) available with higher  
> precision. You may want to read a bit on periodic boundary  
> conditions from Henk Bekker (notably his 1996 JCC paper).
>
> By the way.., don't use the truncated octahedron (unless it's for  
> comparison), try a rhombic dodecahedron instead. It's smaller and  
> most likely better in terms of the simulation results.
>
> Cheers,
>
> Tsjerk
>
> On 3/30/06, Michael Shirts <mrshirts at gmail.com> wrote:
> 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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>
> -- 
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
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