On Mon, Jul 13, 2009 at 11:17 PM, <Charles at schwieters.org> wrote: >> > > How much motion do you see versus that expected for 1ps of simulation at > 500K?
None at all. So it doesn't seem to be an issue of simulation time (even though it's extremely short). But thanks for pointing out that I was only simulating a ps! I guess that means remaining issues with the bond geometry have forced the adaptive time step into very low territory. It's probably time to take a step back and sort things out one after the other... Thanks! Raik > >> For some reason, the energies look very different (unreasonably high >> with high T) when I am re-initializing the system from the PDB that is >> created in the first half of the protocol. But I guess that's an >> unrelated problem that I first have to look into a bit better. > > not sure what's going on there. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkpbpIcACgkQPK2zrJwS/lZudwCcCntYixPwtp4Czs3q7UGXY1xi > KJsAn0JmBdIpEaxmboA+Q6V7YJ4Uxkt1 > =a4lr > -----END PGP SIGNATURE----- >
