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Hello Jie-rong-- > > Thanks for your suggestion. I tried to understand this order.py > script from gb3_ensemble, but there are still some parts that still > confused me. > > The biggest difference I can tell between the script I posted in previous > e-mail and order.py is that there is a Powell minimization following the > dynamics at each temperature during the cooling steps. Is this the feature > that you suggested "can't mix EnsembleSimulaition with XPLOR minimization"? > I don't understand this. Could you explain more? Or some reference > suggested to read? The biggest problem with your script is the direct calling of the XPLOR mini powell statement. This will not work with EnsembleSimulations. The use of DynMin in order.py is probably not necessary. > > You also mentioned "the scaling of energy results in a time scaling, such > that larger ensembles should use longer times for dynamics". Does it mean > that if larger ensemble size is used, the dynamics time should set longer > manually (for example, set finalTime 1 ps to 10 ps )? Or does it mean the > "delta_t" between dynamic steps become shorter when the size of ensemble is > larger, and it takes longer (more computer time, more steps) to reach > finalTime? You may need to manually set finalTime to be a larger value. Please try without doing this first, though. > > In addition, any difference between potList.add, and potList.append, since > both are used in order.py? Thanks a lot!! > There is no difference. potList.append is now preferred, as this is the name of the method used by native Python lists. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJGvhXPK2zrJwS/lYRAr9fAJ9h9oubPlisjVCGib8K596KUxO15QCggQs7 XQhvctOauzBCGjPluvqUay8= =iA6D -----END PGP SIGNATURE-----
