doc updates

- explain change in GROMACS output to ~1e-7
- minor doc fixes

CHANGES

@@ -28,7 +28,9 @@ Fixes
 
 Changes
   - The scipy constant for gas constant is used for parsers instead of the
-  contestants used by the corresponding MD engine (issue #125, PR #129).
+    constants used by the corresponding MD engine (issue #125, PR #129).
+    This leads to small changes in results from GROMACS simulations compared to the 
+    previous releases.
   - Visualisation module will change the data according to input unit (issue
   #125,PR #129).
   - The parser output dataframe with metadata (issue #125, PR #129).
@@ -144,4 +146,3 @@ Features:
     - Subsampler functions for slicing, statitistical inefficiency, equilibration detection.
     - Minimally functional estimators for MBAR, TI.
     - high test coverage (works with data in alchemistry/alchemtests)
-

src/alchemlyb/parsing/amber.py

@@ -274,7 +274,7 @@ def extract_u_nk(outfile, T):
 
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
 
     """
     beta = 1/(k_b * T)
@@ -334,7 +334,7 @@ def extract_dHdl(outfile, T):
 
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
 
     """
     beta = 1/(k_b * T)

src/alchemlyb/parsing/gmx.py

@@ -27,9 +27,23 @@ def extract_u_nk(xvg, T):
         Potential energy for each alchemical state (k) for each frame (n).
 
 
+    Note
+    -----
+    Previous versions of alchemlyb (<0.5.0) used the `GROMACS value of the molar gas constant
+    <https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html>`_
+    of  :math:`R = 8.3144621 \times 10^{−3}\, \text{kJ}\cdot\text{mol}^{-1}\cdot\text{K}^{-1}`
+    instead of the scipy value :data:`scipy.constants.R` (see :mod:`alchemlyb.postprocessors.units`).
+    The relative difference between the two values is :math:`6 \times 10^{-8}`. 
+    
+    Therefore, results in :math:`kT` for GROMACS data will differ between alchemlyb ≥0.5.0 and
+    previous versions; the difference is on the order of :math:`10^{-7}` for typical cases.
+    
+    
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.        
+        This leads to slightly different results for GROMACS input compared to 
+        previous versions of alchemlyb.
 
     """
 
@@ -125,10 +139,24 @@ def extract_dHdl(xvg, T):
     dH/dl : Series
         dH/dl as a function of time for this lambda window.
 
-
+   
+    Note
+    -----
+    Previous versions of alchemlyb (<0.5.0) used the `GROMACS value of the molar gas constant
+    <https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html>`_
+    of  :math:`R = 8.3144621 \times 10^{−3}\, \text{kJ}\cdot\text{mol}^{-1}\cdot\text{K}^{-1}`
+    instead of the scipy value :data:`scipy.constants.R` (see :mod:`alchemlyb.postprocessors.units`).
+    The relative difference between the two values is :math:`6 \times 10^{-8}`. 
+    
+    Therefore, results in :math:`kT` for GROMACS data will differ between alchemlyb ≥0.5.0 and
+    previous versions; the difference is on the order of :math:`10^{-7}` for typical cases.
+    
+    
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
+        This leads to slightly different results for GROMACS input compared to 
+        previous versions of alchemlyb.        
 
     """
     beta = 1/(k_b * T)

src/alchemlyb/parsing/gomc.py

@@ -28,7 +28,7 @@ def extract_u_nk(filename, T):
 
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
 
     """
 
@@ -109,7 +109,7 @@ def extract_dHdl(filename, T):
 
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
 
     """
     beta = 1/(k_b * T)

src/alchemlyb/parsing/namd.py

@@ -28,7 +28,7 @@ def extract_u_nk(fep_file, T):
 
     .. versionchanged:: 0.5.0
         The :mod:`scipy.constants` is used for parsers instead of
-        the contestants used by the corresponding MD engine.
+        the constants used by the corresponding MD engine.
 
     """
     beta = 1/(k_b * T)