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

[Erik Lindahl]

Hi,

Box correction is already done automatically in Gromacs (ns.c) - what  
I meant here was "fairly skewed compared to a rectangular box", e.g.  
30 degrees. Since the charge spreading has to be done on a triclinic  
grid in that case it is no longer radially uniform, which _could_  
affect accuracy a bit (i.e., you might need to user higher  
interpolation order).

Cheers,

Erik



On Mar 30, 2006, at 2:05 PM, Tsjerk Wassenaar wrote:

>
> Hi Erik,
>
> Actually a severely skewed box is basically an imaginary concept.  
> For normal MD dimensions it is always possible to perform a simple  
> transformation to transform a box into one which complies to the  
> Gromacs rules in an optimal way. That is, if the box vector lengths  
> are around the same order of magnitude. Maybe a routine for this  
> could be added to gromacs (editconf/genbox/grompp) to fix skewed  
> boxes, and to optimize the use of PME. I added a routine to my  
> version of pbc.c which could provide a basis. This does not change  
> the system, but only uses other, equally valid, lattice vectors.  
> Let me know if you're interested.
>
> Tsjerk
>
> On 3/30/06, Erik Lindahl <lindahl at sbc.su.se> wrote:
> 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
> +31 50 363 4336
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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
> +31 50 363 4336
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