Add warnings section in docs

Warn users not to run ABFE on membrane proteins with the current version of a3fe, as discussed in #4 .
michellab · Jul 24, 2024 · 80436ae · 80436ae
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diff --git a/docs/index.rst b/docs/index.rst
@@ -13,6 +13,7 @@ Welcome to a3fe's documentation!
    getting_started
    a3fe_design
    guides
+   warnings
    CHANGELOG
    api
 

diff --git a/docs/warnings.rst b/docs/warnings.rst
@@ -0,0 +1,4 @@
+Warnings
+========
+
+ - We do no recommend running ABFE calculations with membrane proteins using the current version of ``a3fe``. This is because SOMD (Sire/ OpenMM Molecular Dynamics, part of Sire) is used for the free energy calculations (after setup with GROMACS), and currently SOMD doesn't support PME and uses an isotropic barostat. We plan to implement support for ABFE with GROMACS in the future.