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Hi Jie-rong-- > > The attachments are the input files that I used. The mailing list doesn't allow large emails- these messages are sent to many people. > > > 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. ) > > > I ran the script and generated 4 ensembles of Ne=8 structures. The average Rg for these was 26.7 +/- 4.0 I then ran two calculations of 4 Ne=1 structures and got Rg= 36.0 +/- 4.3 and 30.0 +/- 3.2 There may be something systematic going on, but it's not too much. Note that this calculation starts with an extended structure with extremely short bonds- not at all near equilibrium. It might be interesting to watch trajectories of these runs. Note also that the Ne=8 average structures are meaningless. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJpHH8PK2zrJwS/lYRAqXvAJ4lnCtdz1e2UgpQBvfBZ8zpJ/x3uQCfX304 MJwvfe9FTbEg27+l55050gw= =8MIV -----END PGP SIGNATURE-----
