add limitations

- GROMACS exclusion/rlist bug
- neutral solutes only (#97)
- mixed solvents

doc/sphinx/source/index.txt

@@ -105,6 +105,27 @@ The version information can be accessed from the attribute
 
 .. _semantic versioning: https://semver.org	      
 
+Limitations and known issues
+----------------------------
+
+For current issues and open feature requests please look through the
+`MDPOW Issue Tracker`_. Some of the major open issues are:
+
+* GROMACS versions < 2021 can silently produce incorrect free energy estimates because exclusions
+  are not properly accounted for 
+  for solutes larger than the rlist cutoff when the ``couple-intramol = no`` decoupling is used
+  (as it is in all of MDPOW), see https://gitlab.com/gromacs/gromacs/-/issues/3403.
+  MDPOW does not detect this situation and does not offer a workaround (namely doing separate 
+  vacuum simulations and use ``couple-intramol = yes``). GROMACS 2021 at least fails when the
+  failure condition occurs (see https://gitlab.com/gromacs/gromacs/-/merge_requests/861).
+* Only free energy calculations of neutral solutes are supported; the workflow also does not 
+  include addition of ions (see issue `#97 <https://github.com/Becksteinlab/MDPOW/issues/97>`_).
+* Mixed solvents (octanol and water) are only supported with the included template topology files
+  for GROMACS >= 2018.
+* Adding new solvents requires modifying the MDPOW code; instead it should be configurable.
+
+
+
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