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Hello-- > I'm running a structure calculation for my protein using a simulated > annealing protocol called refine_rama.inp which is similar to the > /PROT_REFI/sa_dipo_coup_shift.inp protocol available in the xplor-nih- > 2.9.6 version, apart from the use of Verlet dynamics. I'm using > experimental restraints derived from NOEs, backbone dihedral angles, > hydrogen bonds, CA and CB chemical shifts and RDCs together with Da > and R values estimated from the distribution of dipolar couplings. > When I run the structure calculation using the above mentioned > restraints and only NH dipolar couplings I observe a peculiar > behaviour during the high T dynamics steps which should be performed > at 2000 K, that is the temperature increases rapidly during the > dynamics up to 9473 K and then it slowly goes down again down to 2000 > K where it stays for the second half of the high T dynamics. The > cooling steps are performed correctly as far as temperature is > concerned (finalT=100 K), and the final Energies obtained for 30 > structures calculated are in the range 1083-4111 kcal/mol. When I add > to the experimental data the dipolar couplings measured for NC' > vectors, normalized respect to DNH, I observe the same increase in > temperature during the high T dynamics, and even worse, a sudden > increase in T up to 80292 K at the final stages of the cooling step > (I_COOL=123 in the first structure) which compromises the results, in > fact the output 30 structures have Energies in the range 8237-114391. I'd like to help, but no Xplor-NIH does not contain the file sa_dipo_coup_shift.inp or a directory named PROT_REFI. I suggest you upgrade to the latest version (2.9.9), and work from the eginput/protG/anneal.py script as an alternative. > Why are these sudden increase in T observed even if the tcoupling option is > set to true? This is probably due to some instability in the dynamics. > Are the Energy values of the first run (DNH only) reasonable? I'll be very > happy to send as attached files the Xplor outputs. Note that the RDC treatment in the old XPLOR potential terms requires great care, and is quite finicky. I strongly suggest that you use the Python RDC potential interface mentioned above. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD4DBQFCOEFXPK2zrJwS/lYRAtmuAJ9FJ81FEydw2P/8DNGelpnq+6AC4ACY+w97 47mEnYqhgZ+araKK4f5HFg== =VTLL -----END PGP SIGNATURE-----
