On Jan 4, 2012, at 9:19 AM, David Lonie wrote: > If there is an easily parsed / imported / OBConv-ertable database of > structures somewhere, it wouldn't be too difficult to come up with a > test.
I think the question would be "how many molecules do you want?" There's a set of 18 molecules in tests/files/forcefield.sdf and we could certainly make that larger. It's easy enough to get the MMFF94 test file, which has ~700 molecules: http://ccl.net/cca/data/MMFF94/MMFF94_dative.mol2 In developing the "auto-optimize" in Avogadro and some other side-projects here at Pitt, I also have a set of files with stretched bonds, randomly displaced atoms, etc. These are useful since they represent geometries far from the minimum. > Other important factors to test would be the trust radius (max step size) and > step > adjustment factors in the simple line-search -- I'm not sure where the > currently used parameters came from. I eyeballed them, although in the recent months, I've been tinkering to give both better time performance and better convergence. AFAICT, it's a black art to get a good trust radius and adjustment factor. If anyone knows of papers or methods to compute these, I'd be very interested. > In addition to the final energies, it would be interesting to count > calls to Energy() and steepest descent/conjugate gradient cycles are > required. If you're going to do all that, I suggest someone consider writing a BFGS minimizer (which probably would require Eigen): http://en.wikipedia.org/wiki/BFGS_method http://en.wikipedia.org/wiki/Limited-memory_BFGS The BFGS minimizer would certainly converge faster and probably more tolerant of unusual energy surfaces than steepest descent or conjugate gradients. -Geoff ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
