2010-05-24 -- Magdalena A. Jonikas
README file for random unfold example

This example is meant to demonstrate NAST's ability to generate a 
random unfolded RNA structure where only the secondary structure is
constrained.

NAST randomly picks a starting residue and adds residues to each end
one at a time, with MD steps to "minimize" the structure in between.

Each residue is added to random un-obstructed position within a
reasonable distance from it's connecting residue.

Please see the movie 'trna-random-build-demo1.mov' to see a visualization
of this process.

To run the example:
python runUnfoldTest.py

To see examples results, look in the exampleResults directory:
The file 6TNA-RU-last.pdb is the final pdb structure generated by NAST.
The file 6TNA-RU-movie.pdb is a trace of the building process, similar
to the one used to generate the demo movie.

Some options:
verbose = False will prevent the script from spitting out energy details 
at every MD step.
movieOut = False will prevent the script from generating the pdb trace.
numSteps defines how many MD steps are run between each residue addition.	
stepsPerReport defines how often the pdb trace is written out when movieOut 
is not None.

You can string the random unfold and regular NAST MD functions together by
using the output of runRandomUnfold as the input of the regular run command 
used in the 6TNA_MD example.