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Hello Jie-rong-- > I used a modified script from dna_refi/ensemble.py, in which only BOND, ANGL, > IMPR, VDW energies are considered, to test how the random conformers look > like. > > The size of ensemble for 1 and 8 were tested. As you suggested before, the > larger the size of ensemble, the longer dynamics needed. However, even if > the dynamics for 8 conformer is set up to 12 ps (at each cooling > temperature, default in the original script was 0.2 ps), the radius of > gyration of 8 conformer is much smaller than the results from 1 conformer. I > would expect the outcome of calculation without experimental restraint should > be independent of the size of ensemble. (It doesn't change this phenomenon > if RAMA is added. ) > If you could send me the exact script you're using, I will try ti reproduce your results and figure out what's going on. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJowWqPK2zrJwS/lYRApUtAJ4hWiGEFVdntzR4f6W0vkDYcuk9LwCfWfik f42Fs4Cm07lhXYEixvrA1Og= =R7HF -----END PGP SIGNATURE-----
