From: Kevin Boyd Date: Wed, 23 May 2018 00:39:26 +0000 (-0400) Subject: Removed "XXX non-matching atom names" Martini statement. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=cc92b3d0d0ebb75758edfbc9b955d90c09f49a97;p=alexxy%2Fgromacs.git Removed "XXX non-matching atom names" Martini statement. 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 --- diff --git a/docs/user-guide/run-time-errors.rst b/docs/user-guide/run-time-errors.rst index 6cb7fc82ff..edb34c8201 100644 --- a/docs/user-guide/run-time-errors.rst +++ b/docs/user-guide/run-time-errors.rst @@ -375,9 +375,7 @@ the :ref:`coordinate ` file. If there is a mismatch, this 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 `_, the workflow relies on :ref:`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 ` file that has the old (pre-4.5) ion nomenclature. In this case, allowing :ref:`grompp ` to re-assign names is harmless. For just about any other situation, when this error comes up, **it should not be ignored**.