Re: Hexagonal cell and PME grid.

From: Jan Saam (saam_at_charite.de)
Date: Tue Mar 01 2005 - 05:34:17 CST

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Nicholas,

This is correct.

Very nice ACSII graphics by the way!

Jan

Nicholas M Glykos wrote:
> Dear All,
>
> A quick question : I would assume that when using an oblique cell for a
> periodic boundary run, the NAMD PME grid sizes (x,y,z) refer to the
> (possibly non-orthogonal) directions of the cell basis vectors. Is this
> correct ? Just to be on the safe side : in the case of a hexagonal cell
> should the chosen grid should refer to the unit vectors indicated in the
> following "diagram" ? :
>
>
> .v~~\. ,~-~_
> _~^' `^-_ .,~" ``\\.
> .,~' `\\. _~'" `^-_
> _v^' "-v_ .,/' ``\\
> ?' `&" ?.
> | 1 ::
> ? ]' i.
> ? & :.
> | v|-.\\|.~.|-|H~-|-|.~.|-|.~. ::
> ? `? 1 i.
> ? `\ ]' :.
> | \. & |.
> `~v. \. _v~"bb_ ,/'
> ``~_ `\_/^" `*q\. .v~"
> `~\. .,="| ""qo_ ,~''
> `^-__//' `\ ``b\\.v~"
> |' \. T
> | \, |
> | `\ |
> | `\ |
> | |
> | |
> | |
> | |
> `^-_ .,/'
> ``\v. .v-"
> `^-_ ,~''
> ``\\.v~"
> '
>
> Thanks,
> Nicholas
>
>

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