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.holder@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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