Hi Thomas, That's pretty easy. Water-box is just too small. You can increase the water-box size by pressing "Configure" in the main plugin window under the "Water Model" label.
Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > 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 > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
