Using3SPN2

How to use icnf.exe and its different flags

./ icnf.exe <Sequence File> <DNA Type Flag> <Strand Type Flag> <Output Path> <Ions Flag> <Ion Input File - Optional depending on Ions Flag>

DNA Type Flag

0 - B DNA

1 - B DNA Curved

2 - A DNA (Use this model at your own risk. See Documentation PDF section 8 for why.)

Strand Type Flag

0 - Single Strand DNA

1 - Double Strand DNA

Ions Flag

0 - No Ions (Does not require an Ion Input File)

1 - DNA with (Requires an Ion Input File)

2 - DNA in empty box (Requires an Ion Input File)

Example simulations are provided in ~/mylammps/src/USER-3SPN2/examples/