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Hello Lei-- > I am using internal dynamics in my annealing (IVM) protocol. > However,I still see in my output, the angle and bond terms are still > changing dramatically. According to the algorithm, these energies > should not change so much. In the test file in eginput/protG/ > anneal.py.out, the energies does not drift so much.I am wondering > where the problem is and how the program works when they group atoms > together in torsion angle dynamics. I attached part of my output > below. I really appreciate it if you can take a look at it. Looking at your output I see that you have cycle links which the IVM broke in order to do torsion angle dynamics. These broken links correspond to bonds which are not constrained to remain fixed: > > AT_Build::buildNode: cycle link found between atoms 109 TYR 7 CD2 > > and 106 > > TYR 7 CG > > removing bond. I wonder why these cycles exist. Do you have modified residues? Or some nonstandard IVM setup? > Besides, I keep seeing warnings like "Ran out of space. > RESIZING", any idea what is going on? Is it likely a problem? These are informational messages from the nonbonded energy term and can be safely ignored. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGQdy4PK2zrJwS/lYRAgCZAJ4kSi3RbUT0XTk7Mto3Wp2DoSTIBACdG2xB 0BpQpE2iukl3ho9bn9jmJ5U= =BvfN -----END PGP SIGNATURE-----
