-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello Jie-rong-- > > Thank you very much for your reply. I am not sure if I understand you > correctly. Do you mean the final temperature of cooling should be room > temperature (e.g. 298K) instead of 25K in the script? And the high > temperature dynamics at 3000K and cooling starting from 3000K are not changed > in my case? > To start with, just leave the temperatures alone- let's see how large an ensemble is needed for convergence. > Why does the script start from a folded structure instead of extended one? Is > that because there are some "high temperature" steps which can randomly > expand the structure, and therefore it doesn't matter the starting structue > is folded or expanded? > A best initial guess was used in this case. Wildly divergent, expanded conformations were not sampled. > Since I only have PRE data, I commented out "NOE", "dihedral angle > restraints", "repulsive restraints for EDTA-DNA phosphate", "planerity > restraints", and "base-base positional database", and related parameters > (e.g.k_noe) as well. sounds good. You may want the RAMA term. Remove the setup in the .py file, and replace it with: #Rama torsion angle database # import protocol protocol.initRamaDatabase() > Now I am struggled, final lines in the log file is: there may be two problems here. 1) > test.py(569): s.run() > *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.002 > --* > | E(kin)+E(poten)= 21110.576 E(kin)= 4449.966 temperature= > 3238.358 | > | E(poten)= 16660.6104132 grad= nan ANGL= something's wrong with the gradient. Please remove potential terms one at a time to figure out which is causing the nan. I suspect a PRE term. 2) > InternalDynamics::step: caught assertion failure: > calcD_G: singular D matrix. Bad topology? There may also be a topology problem caused by a bad setup of the IVM. Let's fix problem 1) first, though. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIDLPWPK2zrJwS/lYRAuJJAJ9EhzW8YCVDSRFAuVmLdPJ7+8gcmgCfY+4j W2pE2jp913L60FZOLcGsRGk= =5sPb -----END PGP SIGNATURE-----
