On Thu, Mar 15, 2012 at 11:52 AM, Geoffrey Hutchison <[email protected]> wrote: >> I'm a Phd student and I'll have to do 'systematic research of rotors' even >> for much larger molecules. > > You may want to investigate the genetic-algorithm and Monte Carlo weighted > search options in Open Babel (which are used by Avogadro). These can be > accessed from the babel command-line and GUI. > > http://openbabel.org/docs/dev/Command-line_tools/babel.html#generating-conformers-for-structures
I agree with Geoff -- that molecule would generate quite a few conformers, at least 10,000 (the GUI cuts off there -- there are probably many more potential conformers for this flexible of a molecule). I started the search and within seconds the search had consumed over 2GB of RAM to store the conformer data. This is probably what caused your crash -- if I had not stopped avogadro on my system, I would have quickly run out of memory and crashed, too. Unfortunately Avogadro doesn't currently have any utilities to generate this many conformers in a memory efficient way, which would require writing to disk as more conformers generated. Your options here are to use a different search algorithm (random/Monte Carlo or GA) to try just sampling some of the conformational space, or try to find a computer with an enormous RAM reserve. If you really do need to generate all 10,000+ conformers, you'll probably need to use the commandline openbabel interface. The Avogadro interface is only capable of generating 10,000 conformers. I doubt that the raw babel CLI interface has such a restriction, but I'm not 100% sure on that. Hope this helps, Dave ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Avogadro-Discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
