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Hello Raik-- > >>> The default settings for the Python interface are for structure > >>> determination calculations- they are not appropriate for realistic MD > >>> calculations. Moreover, you will need some description of the solvent to > >>> obtain qualitatively realistic results. You will probably want to > >>> replace the RAMA term with the DIHE term. You should not want to call > >>> massSetup(). > >> our IVM dynamics is, in principal, working now and I am trying to make > >> the motions a bit more realistic. Are there any example scripts > >> (python or classic) that use IVM for non-restrained dynamics (if > >> possible with Langevin heat coupling)? I have many scripts with > >> param19 based setup for cartesian MD but param19 may not be the best > >> parameters for IVM... > >> > > > > Sorry, I really haven't tried to do this sort of calculation. Are you > > going to account for the solvent in some way? > > Given the other approximations, I first wanted to see how far we get with a > simple distance-dependent dielectric. Our first aim is to see what > conformations > are at all accessible. So thorough sampling is more important than an acurate > ensemble. Having both at once would of course be great but I guess we will > eventually have to play around with some kind of umbrella sampling or > monte-carlo moves to get there. Is param19 at all suiteable for IVM > sampling? > param19 should probably work fine with torsion angle dynamics. Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkpk3VgACgkQPK2zrJwS/lZHJwCfbWWklxrmGN5vnEaKTpnnPJrj c2QAn2e5zx+yjlZ/8YLWUlHpCDdSSzXy =zVeu -----END PGP SIGNATURE-----
