Dear Charles, 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? 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? In addition, any difference between potList.add, and potList.append, since both are used in order.py? Thanks a lot!! Best wishes, Jie-rong 2008/11/6 <Charles at schwieters.org> > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Jie-rong-- > > > I am trying to use ensemble calculation for unstructured proteins. > However, > > the output structures are too compact than expected, so I did the > following > > test: > > You can't mix EnsembleSimulations with the XPLOR minimization > routines. This is one problem. You should work from a more modern > starting script, such as eginput/dna_refi/ensemble.py or > eginput/gb3_ensemble/order.py. > > For evaluation of the output, you can directly compare energies- are the > Ne=7 energies lower than those for Ne=1? > > Finally, the scaling of energy results in a time scaling, such that > larger ensembles should use longer times for dynamics. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iD8DBQFJE0dxPK2zrJwS/lYRAhYTAJ9GsjIHjMZwyTscu3giA7dNBZseHgCfQKh4 > r3UH6MTIyk8hzHURZ8kfLZM= > =X358 > -----END PGP SIGNATURE----- > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20081111/2998e313/attachment.html
