Verified oxDNA with modified nucleotide layout

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

examples/USER/cgdna/examples/duplex1/data.duplex1

...ples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.1

...ples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.4

examples/USER/cgdna/examples/duplex2/data.duplex2

...ples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.1

...ples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.4

examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1

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

...ER/cgdna/examples/oxDNA/duplex1/log.17Mar17.duplex1.g++.1

...ER/cgdna/examples/oxDNA/duplex1/log.17Mar17.duplex1.g++.4

examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2

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

...ER/cgdna/examples/oxDNA/duplex2/log.17Mar17.duplex2.g++.1

...ER/cgdna/examples/oxDNA/duplex2/log.17Mar17.duplex2.g++.4

src/USER-CGDNA/bond_oxdna2_fene.cpp

src/USER-CGDNA/bond_oxdna2_fene.h

src/USER-CGDNA/bond_oxdna_fene.cpp

src/USER-CGDNA/bond_oxdna_fene.h

src/USER-CGDNA/mf_oxdna.h