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Update Autosolvate tutorial_multicomponent.rst
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Patrick Li committed Jun 28, 2024
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Expand Up @@ -4,6 +4,18 @@ The following tutorial illustrates the basic usage of ``Autosolvate Multicompone

There will be one example systems: naphthalene in mixed water and acetonitrile solvent. The tutorial will be broken down into three steps:

.. note::

Note::

Note to Autosolvate Developers

I have not tested if the download links work properly in this document because I can not add this .rst file to https://autosolvate.readthedocs.io/en/latest/.

Please test and make sure all the download link work properly.



Prerequisites
-------------------------------------------
Once you have AutoSolvate and all dependencies installed you will need the pdb files for solute and solvents. Mak sure run the example in its own directory to have clear separation of files.
Expand Down Expand Up @@ -101,7 +113,7 @@ The first step is putting the solute in the solvent box, which uses the ``boxgen

Note::
note to Autosolvate Developers
Note to Autosolvate Developers

(1) Please test if '-m' and '-s' command fully support both xyz and pdb file inputs which means if someone provides xyz file, the Multicomponent module will convert the xyz file into pdb file using openbable.

Expand Down Expand Up @@ -328,7 +340,7 @@ With these three files (``MYBOX.inpcrd``, ``MYBOX.prmtop``, ``MYBOX.pdb``), we a

Note::

note to Autosolvate Developers
Note to Autosolvate Developers

There are many flags in startmulticomponent() not working.

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