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Hello Lei-- > I am writing to ask a very basic questions of torsion > angle dynamics. I am wondering how the equations of motion are > integrated in the simulation. My concern is the way to calculate the > derivative of the energy terms with respect to torsion angle. I read > some literature but not full understand all. Is it very convenient to > calculate this derivative when we already know the derivative of > energy with respect to the cartesian coordinates? > The reason I am asking is that I am using an external > potential in python. I only provide the way to calculate energy from > cartesian coordinates and the derivative of energy with respect to > cartesian coordinates. It really concerns me whether I am able to use > the IVM module correctly. the IVM expects gradients with respect to cartesian atomic coordinates- so I think you're calculating the correct quantity. Derivatives with respect to torsion angles can be used within the IVM - internally, but i have not yet made an external interface to these. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGirOWPK2zrJwS/lYRAlcWAJ48w5HzX06L+Q5CFoV0uZfsG15YSQCfSYU4 i2gIZ7ehatcdJia9ExRESzE= =/s69 -----END PGP SIGNATURE-----
