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Hello Ryan-- > > I'm trying to understand why I would use one or the other. The two are > often both used in example scripts. > > For example: > > from ivm import IVM > test1 = IVM(); > test2 = test1; > > from protocol import initDynamics > run1 = initDynamics( test1, [ARGS1] ) > > from simulationTools import AnnealIVM > run2 = initiDyanmics( [ARGS2], ivm = test2, [ARGS3] ) > > run1.run() > run2.run() > this code will not execute, as initDynamics() does not return a value - it serves only to set up IVM parameter appropriate for dynamics (as opposed to minimization). AnnealIVM (which you actually don't use in the above example) is used to perform an entire simulated annealing cooling loop. The IVM object passed should probably be initialized for dynamics before running the loop. The loop will then call the IVM object's run() method many times to perform MD as each temperature. I hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDobs0PK2zrJwS/lYRAiKWAJ9/2kXXUr7cOk5e75xb9egkbCisSQCbBnqa F+rPjgtj/DOoTf5AOrbfTCc= =qohb -----END PGP SIGNATURE-----
