Charles at schwieters.org wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Raik-- > >> Charles at schwieters.org wrote: >>> 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? Thanks a lot! Greetings, Raik > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkpg4w8ACgkQPK2zrJwS/lafVwCeKtPYjNPuMNAos3FyNE1VD/K0 > tJAAnR0CTmXeUx/bkGB7A8wzxHLU/6Ru > =sGpc > -----END PGP SIGNATURE----- > -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________
