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Hello Nah-- > Is there an example/sample python script that performs just a simple SA > (something like random.inp) ? the nice examples (anneal.py & refine.py) > provided in the eginputs dir are great, yet, a simple SA script ( load > structure, generate extended conformation, add basic potentials (just Xplor > ones - ANGL,BOND,VdW, etc., maybe the knowledge-based ones - RAMA,COLL) do a > simple SA from 3000k to 50k, will help me a great deal in understanding more. > sorry- this is what we have for now. > Also, an explanation for the purpose of doing something like in anneal.py > (from gb1_rdc) for example, why high-temperature TA dynamics, cooling steps > and low temp minimization in Cartesian coordinates ( role of ramping up some > params and the corresponding use of helper functions,classes etc.,) - what > happens if this is not done ? Can one get convergence just with a SA in TA or > Cartesian space etc., are some other things where the inputs will be > appreciated. The Xplor manual (with examples only using xplor interface) > doesn't help much the one who is getting started from the Xplor-Python > interface. And the python example scripts,as such, though easier to > understand/emulate introduce many things, which are better understood and > used rather than just emulated. Some more basic examples will help here. > The protocols have been refined over the (many) years to optimize convergence and minimize computational effort. Other groups use different algorithms, and we're very interested if someone comes up with a better protocol. I hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIDQQOPK2zrJwS/lYRAho+AKCIEHvMvDzoLZJILmt/CjL8JFfLRQCcCbp/ t6EP+gg69ixTx3fn+9QKJdI= =2tTn -----END PGP SIGNATURE-----
