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Updated tests and documentation, added warning message

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This commit is contained in:
Oliver Henrich
2021-07-19 11:22:06 +01:00
parent b7a17dc25d
commit 15b3b6445e
47 changed files with 19656 additions and 19382 deletions
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doc/src/bond_oxdna.rst
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@ -86,12 +86,11 @@ commands:
.. 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>`.
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