Hey :)
I guess you tried the plugin with something quite small, using a too small
distance between periodic images. This should be caught off by a check in
the plugin, resetting the simulation cell if the usual criteria result in a
too small one. The best way, IMHO, is checking the last line of the .gro
file obtained with editconf and replacing it by a 3.0 nm rhombic
dodecahedron or cube. Not sure what the default box type is, but it should
be a rhombic dodecahedron :) I notice from the log that a rectangular cell
was used.
Cheers,
Tsjerk
On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder <thomas.hol...@schrodinger.com
> wrote:
> Hi Tomasz,
>
> Tomasz Makarewicz wrote, On 08/01/13 09:36:
> > Thanks for the report. Could you send me file
> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output,
> so
> > we will be able to analyse, what exactly GROMACS is missing.
>
> The relevant error seems to be:
>
> ERROR 1 [file foo.top, line 710]:
> ERROR: The cut-off length is longer than half the shortest box vector
> or longer than the smallest box diagonal element. Increase the box
> size or decrease rlist.
>
> Full log:
> http://pymol.org/tmp/dynamics-log.txt
>
> Cheers,
> Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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