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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-----
