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.
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.
Thanks.
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