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Hello Jie-rong-- > > I would like to go back to your earlier suggestions: "properly include > solvent", "appropriate > temperature", and "how large an ensemble is needed for convergence". Could > you give me more details? > I would first look at getting appropriate ensemble size. Recall, you have two sets of ensembles, one for the chromophore, and another describing your protein structure. You should probably first increase the size of the chromophore ensemble until the results converge - to get the appropriate size. Then do the same thing with your structure ensemble. > Besides, I took the "collapse" part off, because the calculated structure > would be "too compact" for a > denatured protein with it. Or I should keep it with better restraint setup? I agree- the Rg term is likely not appropriate. Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIF0yUPK2zrJwS/lYRAgP1AJwJDeJxOSZv2sUacL8Ux5c+5miLPgCfdS0P sqXMTGXfJlXKKExvJm+Ksb0= =UMjs -----END PGP SIGNATURE-----
