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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