Edited the README.md file for the OPLSAA examples.

Author: jewettaij

examples/all_atom/force_field_OPLSAA/README.md

@@ -22,26 +22,6 @@ This will protect you from force-field parameter changes, and you
 will be able to continue using your existing atom and bonded type names safely.
 
 
-### Optional: Duplicate dihedrals, angles, and bonds
-
-Sometimes, even after you have specified the (OPLSAA-specific) atom types
-for the atoms in your molecule, there may be multiple possible choices
-of dihedral, angle, or bond interactions between those atoms
-available in OPLSAA force field (stored in the "oplsaa.lt" file).
-When that happens, moltemplate.sh will *attempt to make a reasonable guess*,
-chosing the original (oldest, most common) version of the interaction between
-those atom types.  However, you can override this choice:
-
-- The new (2023) version of OPLSAA contains many additional choices for your dihedral, angle, and bond interactions.  This gives you an opportunity to improve your simulation accuracy, but it also requires more effort on your part.  To see the list of choices, you must now run moltemplate with the "-report-duplicates bytype __" arguments.  For example:
-```
-moltemplate.sh  system.lt  -report-duplicates bytype __
-```
-- If you see a file named "warning_duplicate_dihedrals.txt", "warning_duplicate_angles.txt", "warning_duplicate_bonds.txt", or "warning_duplicate_impropers.txt" after running moltemplate, then it might be a good idea to read the first few warning messages
-in those files and modify your .lt files accordingly (for example, by adding a custom "Data Dihedrals" section).  Several example .lt files demonstrate how to do that, including:
-- butane/moltemplate_files/butane.lt
-- benzene+benzoic_acid/moltemplate_files/benzoic_acid.lt
-
-
 
 
 ### Atomic charges
@@ -55,6 +35,7 @@ LT files will be ignored.)*
 **These charges can be overridden.**
 
 
+
 ### Customizing atomic charges in OPLSAA molecules
 
 #### Background information
@@ -108,6 +89,27 @@ of the [spce.lt](waterSPCE+methane/moltemplate_files/spce.lt) file.
 
 
 
+### Optional: Duplicate dihedrals, angles, and bonds
+
+Sometimes, even after you have specified the (OPLSAA-specific) atom types
+for the atoms in your molecule, there may be multiple possible choices
+of dihedral, angle, or bond interactions between those atoms
+available in OPLSAA force field (stored in the "oplsaa.lt" file).
+When that happens, moltemplate.sh will *attempt to make a reasonable guess*,
+chosing the original (oldest, most common) version of the interaction between
+those atom types.  However, you can override this choice:
+
+- The new (2023) version of OPLSAA contains many additional choices for your dihedral, angle, and bond interactions.  This gives you an opportunity to improve your simulation accuracy, but it also requires more effort on your part.  To see the list of choices, you must now run moltemplate with the "-report-duplicates bytype __" arguments.  For example:
+```
+moltemplate.sh  system.lt  -report-duplicates bytype __
+```
+- If you see a file named "warning_duplicate_dihedrals.txt", "warning_duplicate_angles.txt", "warning_duplicate_bonds.txt", or "warning_duplicate_impropers.txt" after running moltemplate, then it might be a good idea to read the first few warning messages
+in those files and modify your .lt files accordingly (for example, by adding a custom "Data Dihedrals" section).  Several example .lt files demonstrate how to do that, including:
+- butane/moltemplate_files/butane.lt
+- benzene+benzoic_acid/moltemplate_files/benzoic_acid.lt
+
+
+
 ### Minor issue: Improper angles
 
 The style of improper interaction used by OPLS force fields depends on an angle which depends on the order of the atoms surrounding the central atom. When multiple atoms have the same type, this creates ambiguity in atom order. Since there is no guarantee that moltemplate will choose the same atom order as other molecule builders (such as VMD), this can lead to small unavoidable discrepancies in energies and forces computed by LAMMPS and NAMD.  But their effect should be neglegible.