[gmx-developers] walls and pbc setting in CVS code

Makoto Yoneya makoto-yoneya at aist.go.jp
Tue Aug 26 02:19:55 CEST 2008

Dear Prof. Berk Hess and GROMACS developers:

Thanks a lot for the comments.
(Sorry, I'd sent the junk post just before this
by mistake.)

> The error message tells you (nearly) everything.
> I guess you have a very small box and you have a high 
> lincs_order and/or lincs_iter.
> The error message tells you what to do.
> Use -rcon
> and/or decrease lincs_order and/or lincs_iter or increase the 
> box size.
> Berk

After the successful single processor run with walls and pbc=xy,
the z-component of the box size (initially non-zero value) was 
reset to zero in the output coordinate file (.gro file).
I'm wondering that pbc=xy internally makes z-component box size
to zero, and this prevents somehow to parallel run (and result in the 
error massage related on box size) to initialize.
Again, the initial box size and lincs setting works well with the
same run with just changing pbc=xyz (these should be specially
change for pbc=xy?).
I hope the above will not a junk mail again in this time.

Best regards.

Makoto Yoneya, Dr.
AIST Japan

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