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Axel Kohlmeyer
2021-07-20 18:14:02 -04:00
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doc/src/bond_oxdna.rst
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@ -84,6 +84,13 @@ commands:
the bond topology in the data file. The first (second) atom in a bond definition
is understood to point towards the 3'-end (5'-end) of the strand.
.. warning::
If data files are produced with :doc:`write_data <write_data>`, then the
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
Otherwise the data files will not have the same 3'-to-5' polarity as the
initial data file. This limitation does not apply to binary restart files
produced with :doc:`write_restart <write_restart>`.
Example input and data files for DNA and RNA duplexes can be found in
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python