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Hello Jakob-- > > I would like to implement a new potential using the PyPot base class. > Sorry if this is obvious, but could you explain in a little more > details what calcEnergyAndDerivList should be doing: the derivative > with respect to each atom coordinate?? Actually is it possible to > somehow skip the derivative definition and use some default rather, > because the potential I consider implementing is complicated? > Please follow the example from the tutorial http://nmr.cit.nih.gov/xplor-nih/doc/current/python/tut.pdf (page 41) The derivs variable in calcEnergyAndDerivs is a sequence object whose elements coorespond to gradient of the energy with respect to atom positions. You could implement the gradient using finite difference, but it will slow things down even more. Xplor-NIH does not provide a utility for doing this automatically. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwzcgAACgkQPK2zrJwS/lZgFACgggOqafKoPSn3P9IaTEXrt35X pz4An2SbvZLstvI3ClAVQ7uMiSufud6+ =FyaZ -----END PGP SIGNATURE-----
