Hexagonal cell and PME grid.

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Tue Mar 01 2005 - 05:17:44 CST

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 

-- 
            Dr Nicholas M. Glykos, Department of Molecular 
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
     Tel ++302551030620 (77620),  http://www.mbg.duth.gr/~glykos/

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