Prmset_cgDNA+_CGF_10mus_int_12mus_ends.mat (Use this for DNA) 
--- Parameterset for DNA with 10 mus simulation for interior blocks and 12 mus for each ends
--- cgFrame for frame fitting
--- TIP3P water model, JC ion model and BSC1 force field
--- Max entropy computation for prmsets
--- used full covariance matrix not truncated
--- Positive definite reconstruction for all sequences (upto 12 mers)

Di_hmethyl_methylated-hemi_combine.mat 




cgDNA+_Curves_BSTJ_10mus_FS.mat
-- same as above except CURVEs+ instead of cgFrame

Prmset_cgRNA+_OL3_CGF_10mus_int_12mus_ends.mat
--- Parameterset for RNA with 10 mus simulation for interior blocks and 12 mus for each ends
-- OL3 forcefiled
-- same water and ion model as above
-- same training library as above
--- cgFrame for frames
--- only GC ends 
-- Alphabets in the parametersets are still ATCG for coding purposes.
-Trimer NPDE 
    'ATA' 
    'ACA'
    'TCA'
    'TAA'
    'TTG'



cgHYB+_CGF_OL3_BSC1_10mus_FS_GC_ends.mat
Note that 
a) only for GC ends but more important there is no symmetry relation between 5' and 3' GC ends
b) Similarly all 16 dimers are independent .. no symmetry relation
c) OL3 forcefiled for RNA strand and TIP3P for DNA strand
d) -- same water and ion model as above
-- same training library as above but no palindromic symmetry
--- cgFrame for frames
-- Alphabets in the parametersets are still ATCG for coding purposes.


