The current statement is that atom renaming in grompp is part of the
accepted workflow, and so the above error can be ignored. Not sure how
long ago this was the case, but I'm fairly certain it isn't now.
Change-Id: Ie4f00bf49d0108c36b5f47b59942b455bba8cd28
To remedy the problem, make sure that the contents of your ``[ molecules ]`` directive
matches the exact order of the atoms in the coordinate file.
To remedy the problem, make sure that the contents of your ``[ molecules ]`` directive
matches the exact order of the atoms in the coordinate file.
-In some cases, the error is harmless. For example, when running simulations with the
-`MARTINI force field <http://cgmartini.nl/>`_, the workflow relies on :ref:`grompp <gmx grompp>` to apply the
-correct names, which are not previously assigned. Also, perhaps you are using a
+In a few cases, the error is harmless. Perhaps you are using a
:ref:`coordinate <gmx-structure-files>` file that has the old (pre-4.5) ion nomenclature.
In this case, allowing :ref:`grompp <gmx grompp>` to re-assign names is harmless.
For just about any other situation, when this error comes up, **it should not be ignored**.
:ref:`coordinate <gmx-structure-files>` file that has the old (pre-4.5) ion nomenclature.
In this case, allowing :ref:`grompp <gmx grompp>` to re-assign names is harmless.
For just about any other situation, when this error comes up, **it should not be ignored**.