Added sequence-dependent stacking and base-pairing strength

doc/src/PDF/USER-CGDNA-overview.pdf

doc/src/pair_oxdna.txt

doc/src/pair_oxdna2.txt

examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1

...ER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1

...ER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4

examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2

...ER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1

...ER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4

examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1

...R/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1

...R/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4

examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2

...R/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1

...R/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4

src/USER-CGDNA/pair_oxdna_hbond.cpp

src/USER-CGDNA/pair_oxdna_hbond.h

src/USER-CGDNA/pair_oxdna_stk.cpp

src/USER-CGDNA/pair_oxdna_stk.h