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Added warning message in documentation and dsDNA ring test in examples

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Oliver Henrich
2021-07-16 12:57:21 +01:00
parent 2a61f72790
commit b7a17dc25d
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doc/src/bond_oxdna.rst
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@ -84,6 +84,14 @@ 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::
LAMMPS has per se no concept of bond directionality. This means the bond definition
(i.e. the sequence of atom IDs) in data files produced with :doc:`write_data <write_data>`
can be different from the one provided in your initial data file. If this is the case,
then the correct 3' to 5' polarity needs to be restored before using the 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