renamed "oplsaa.lt"-->"oplsaa2023.lt" and updated the examples and documentation. The existing "oplsaa.lt" file (and its associated files) still exists. But when users import "oplsaa.lt", moltemplate will create a file named "WARNING_PLEASE_USE_oplsaa2023.lt_INSTEAD.TXT", warning them that "oplsaa.lt" will be deleted in the near future.

Author: jewettaij

doc/moltemplate_manual_src/moltemplate_manual.tex

@@ -2613,7 +2613,7 @@ \subsection{Bonded interactions \textit{by type}}
 commands,
 as well as force field parameters and related atom type properties.
 It's also a good idea to store force-field objects in a separate file
-(eg ``forcefield.lt'', ``oplsaa.lt'', ``gaff2.lt'', ``compass.lt'', etc...)
+(eg ``forcefield.lt'', ``oplsaa2023.lt'', ``gaff2.lt'', ``compass.lt'', etc...)
 so that these rules and parameters can be be applied to different molecules
 more easily (by using the \textit{import} command to load the file when needed).
 
@@ -2905,7 +2905,7 @@ \subsection{``In Charges''}
   %Some force fields (such as the current implementation of OPLSAA and LOPLSAA)
   %assign atom charge according to atom type.
 For example, here is an excerpt
-from the ``loplsaa.lt'' file (on 2020-8-09):
+from the ``loplsaa2023.lt'' file (on 2020-8-09):
 \begin{verbatim}
 write_once("In Charges") {
   set type @atom:80L charge -0.222 # "Alkane CH3- (LOPLS)"
@@ -2983,7 +2983,7 @@ \subsection{``Data Charge By Bond''}
 
 \subsection{The \textit{force\_fields} directory}
 \label{sec:moltemplate_path}
-Files containing popular force fields (like ``oplsaa.lt'' and ``gaff2.lt'')
+Files containing popular force fields (like ``oplsaa2023.lt'' and ``gaff2.lt'')
 and molecule models (like ``spce.lt'') are stored in the ``force\_fields/''
 subdirectory distributed with moltemplate.  (This directory is included when
 you download moltemplate using either git or pip.)
@@ -3088,7 +3088,7 @@ \subsection{Extending an existing force field}
 \end{verbatim}
 
 Incidentally, this is how the LOPLS force field was implemented.
-See \href{https://github.com/jewettaij/moltemplate/blob/master/moltemplate/force_fields/loplsaa.lt}{\tt loplsaa.lt}.
+See \href{https://github.com/jewettaij/moltemplate/blob/master/moltemplate/force_fields/loplsaa2023.lt}{\tt loplsaa2023.lt}.
 
 
 \textit{
@@ -4632,7 +4632,7 @@ \subsubsection{Multiple inheritance:}
 \textit{multiple} different force-field parents:
 \begin{verbatim}
 import "trappe1998.lt"
-import "oplsaa.lt"
+import "oplsaa2023.lt"
 
 Butane inherits TraPPE OPLSAA {
   ...

examples/all_atom/force_field_AMBER/benzene/README.md

@@ -22,7 +22,7 @@ Benzene inherits GAFF { ... }    # (see "benzene.lt")
 
 ### *WARNING: The atomic charges in this examples are not correct*
 
-The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa.lt" file](../../../../moltemplate/force_fields/oplsaa.lt).  Do not do this!)
+The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa2023.lt" file](../../../../moltemplate/force_fields/oplsaa2023.lt).  Do not do this!)
 
 The generation of atomic partial charges requires 3rd party software.
 

examples/all_atom/force_field_AMBER/ethylene+benzene/README.md

@@ -12,7 +12,7 @@ The number of molecules, positions, and simulation box size can be controlled by
 
 ### *WARNING: The atomic charges in this examples are not correct*
 
-The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa.lt" file](../../../../moltemplate/force_fields/oplsaa.lt).  Do not do this!)
+The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa2023.lt" file](../../../../moltemplate/force_fields/oplsaa2023.lt).  Do not do this!)
 
 The generation of atomic partial charges requires 3rd party software.
 

examples/all_atom/force_field_AMBER/hexadecane/README.md

@@ -11,7 +11,7 @@ The number of molecules and simulation box size can be controlled by editing the
 
 ### *WARNING: The atomic charges in this examples are not correct*
 
-The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa.lt" file](../../../../moltemplate/force_fields/oplsaa.lt).  Do not do this!)
+The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa2023.lt" file](../../../../moltemplate/force_fields/oplsaa2023.lt).  Do not do this!)
 
 The generation of atomic partial charges requires 3rd party software.
 

examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README.md

@@ -18,7 +18,7 @@ The number of molecules, positions, and simulation box size can be controlled by
 
 ### *WARNING: The atomic charges in this examples are not correct*
 
-The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa.lt" file](../../../../moltemplate/force_fields/oplsaa.lt).  Do not do this!)
+The AMBER for field does not include charge information.  (In this example, they were borrowed from the corresponding atoms in the ["oplsaa2023.lt" file](../../../../moltemplate/force_fields/oplsaa2023.lt).  Do not do this!)
 
 The generation of atomic partial charges requires 3rd party software.
 

examples/all_atom/force_field_OPLSAA/README.md

@@ -6,18 +6,18 @@ There is no guarantee that simulations prepared using moltemplate will reproduce
 
 
 
-### Suggestion: Make a local copy of the "oplsaa.lt" file
+### Suggestion: Make a local copy of the "oplsaa2023.lt" file
 
 WARNING: The OPLSAA force field changes slightly over time.
 When it happens, it can cause the names of the
 @atoms, @bonds, @angles, and @dihedrals types to change.
 This could break backward compatibility,
 and cause moltemplate.sh to fail when reading your .lt files.
 So if you are using OPLSAA, it's a good idea to make a backup copy of the
-[oplsaa.lt file](../../../moltemplate/force_fields/oplsaa.lt)
+[oplsaa2023.lt file](../../../moltemplate/force_fields/oplsaa2023.lt)
 (located in the
 [moltemplate/force_fields/](../../../moltemplate/force_fields/) folder).
-Copy it to the folder with your other .lt files for the simulation you are working on.  (Moltemplate will look in the local folder first for all the .lt files that it needs, including "oplsaa.lt".)
+Copy it to the folder with your other .lt files for the simulation you are working on.  (Moltemplate will look in the local folder first for all the .lt files that it needs, including "oplsaa2023.lt".)
 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.
 
@@ -29,7 +29,7 @@ will be able to continue using your existing atom and bonded type names safely.
 In most of the OPLSAA examples,
 the atomic charges are determined by their @atom types
 *(...according to a lookup table located at the beginning of the
-["oplsaa.lt"](../../../moltemplate/force_fields/oplsaa.lt) file)*.
+["oplsaa2023.lt"](../../../moltemplate/force_fields/oplsaa2023.lt) file)*.
 *(Any atomic charges listed in the "Data Atoms" section of your molecule's
 LT files will be ignored.)*
 **These charges can be overridden.**
@@ -49,7 +49,7 @@ moltemplate.sh, and later read by LAMMPS.)*
 2) **Specify charges using "set" commands.**
 *(This is how the OPLSAA atom charges are specified.
 After running moltemplate, atom charge information in the
-["oplsaa.lt" file](../../../moltemplate/force_fields/oplsaa.lt)
+["oplsaa2023.lt" file](../../../moltemplate/force_fields/oplsaa2023.lt)
 is copied into the "system.in.charges" file created by moltemplate.sh.
 A LAMMPS input script file (eg. "run.in.nvt" or "run.in.npt")
 is included with all of the OPLSAA examples.  It tells LAMMPS to read
@@ -58,15 +58,15 @@ This overrides the atom charges from the "system.data" file.)*
 
 
 #### How to customize atomic charge
-*(without modifying "oplsaa.lt")*
+*(without modifying "oplsaa2023.lt")*
 
 1) If you use use a 3rd-party program to calculate each atom's charge, you can
 copy those charges into the "Data Atoms" section of your molecule's LT files.
 To prevent LAMMPS from ignoring these charges, delete or comment-out the line
 containing: **"include system.in.charges"** from your LAMMPS input script
 (such as "run.in.min", "run.in.nvt", and "run.in.npt").
 2) Alternatively, if you only want to override the charges of *some* of the
-atoms in your molecules (and use default "oplsaa.lt" charges for the remaining
+atoms in your molecules (and use default "oplsaa2023.lt" charges for the remaining
 atoms), then you can do this by adding an "In Charges" section to your LT file
 and providing a list of custom charges for the \$atoms you want to modify.
 This is demonstrated in the ["graphene_nh2.lt"](functionalized_nanotubes_NH2/moltemplate_files/graphene_nh2.lt)
@@ -94,7 +94,7 @@ of the [spce.lt](waterSPCE+methane/moltemplate_files/spce.lt) file.
 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).
+available in OPLSAA force field (stored in the "oplsaa2023.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:

examples/all_atom/force_field_OPLSAA/alkane_chain_single/README.md

@@ -30,11 +30,11 @@ I suggest starting with the [butane](../butane) example instead.
 
 ### Details
 
-The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains, use the LOPLSAA force-field.  As with all of the OPLSAA examples, when we define these molecules, we only specify the atom names, bond list, and coordinates.  We do not have to list the atom charges, angles, dihedrals, or impropers.  The rules for creating atomic charge and angle topology are contained in the ["loplsaa.lt"](../../../../moltemplate/force_fields/loplsaa.lt) and  ["oplsaa.lt"](../../../../moltemplate/force_fields/oplsaa.lt) files.  To let moltemplate know that you want to use these rules, define your molecules (and molecular subunits) this way:
+The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains, use the LOPLSAA force-field.  As with all of the OPLSAA examples, when we define these molecules, we only specify the atom names, bond list, and coordinates.  We do not have to list the atom charges, angles, dihedrals, or impropers.  The rules for creating atomic charge and angle topology are contained in the ["loplsaa2023.lt"](../../../../moltemplate/force_fields/loplsaa2023.lt) and  ["oplsaa2023.lt"](../../../../moltemplate/force_fields/oplsaa2023.lt) files.  To let moltemplate know that you want to use these rules, define your molecules (and molecular subunits) this way:
 
 
 ```
-import "loplsaa.lt"
+import "loplsaa2023.lt"
 CH2 inherits OPLSAA { ... }         # (see "ch2group.lt")
 CH3 inherits OPLSAA { ... }         # (see "ch3group.lt")
 Alkane50 inherits OPLSAA { ... }    # (see "alkane50.lt")
@@ -43,15 +43,15 @@ Alkane50 inherits OPLSAA { ... }    # (see "alkane50.lt")
 
 #### OPLSAA or LOPLSAA"?
 
-There are only a few differences between LOPLSAA and OPLSAA.  The LOPLSAA force field contains a few extra atom types and dihedral interactions which improve the accuracy of long alkane chains.  The ["loplsaa.lt"](../../../../moltemplate/force_fields/loplsaa.lt) file (referenced above) incorporates these extra atom and dihedral types in the existing OPLSAA force field *instead* of creating a new force field named "LOPLSAA".  *(There is no separate "LOPLSAA" force field object.  I apologize if this is confusing.)*  You can mix LOPLSAA and OPLSAA atoms in the same molecule.
+There are only a few differences between LOPLSAA and OPLSAA.  The LOPLSAA force field contains a few extra atom types and dihedral interactions which improve the accuracy of long alkane chains.  The ["loplsaa2023.lt"](../../../../moltemplate/force_fields/loplsaa2023.lt) file (referenced above) incorporates these extra atom and dihedral types in the existing OPLSAA force field *instead* of creating a new force field named "LOPLSAA".  *(There is no separate "LOPLSAA" force field object.  I apologize if this is confusing.)*  You can mix LOPLSAA and OPLSAA atoms in the same molecule.
 
 
 
 ### Customizing atomic charges
 
 In this example, atomic charge for OPLSAA atoms is determined by @atom type
 *(...according to a lookup table located at the beginning of the
-["oplsaa.lt"](../../../moltemplate/force_fields/oplsaa.lt) file)*.
+["oplsaa2023.lt"](../../../moltemplate/force_fields/oplsaa2023.lt) file)*.
 *(Any atomic charges listed in the "Data Atoms" section of your molecules'
 LT files will be ignored.)*
 **These charges can be overridden.**

examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2.lt

@@ -4,15 +4,15 @@
 # This file is located in the "force_fields" subdirectory
 # distributed with moltemplate.
 
-import "loplsaa.lt"   # <-- defines the standard "OPLSAA" force field as well as
+import "loplsaa2023.lt"   # <-- defines the standard "OPLSAA" force field as well as
                       #     custom parameters for long alkane chains taken from
                       #     Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 
 		      #     To use the ordinary OPLSAA force field parameters,
 		      #     (instead of the Sui et al. parameters), change the
 		      #     atom types below from "@atom:57L","@atom:60LCH2" to
-		      #     "@atom:57" and "@atom:60"  (defined in "oplsaa.lt")
+		      #     "@atom:57" and "@atom:60"  (defined in "oplsaa2023.lt")
 
-# The "loplsaa.lt" and "oplsaa.lt" files are located at:
+# The "loplsaa2023.lt" and "oplsaa2023.lt" files are located at:
 # https://github.com/jewettaij/moltemplate/tree/master/moltemplate/force_fields/
 # If you want to customize these files, download them and copy them to this folder.
 
@@ -34,13 +34,13 @@ CH2 inherits OPLSAA {
     $bond:ch2 $atom:c $atom:H2
   }
 
-  # Atom type numbers (@atom:57L,@atom:60LCH3) are defined in "loplsaa.lt",
+  # Atom type numbers (@atom:57L,@atom:60LCH3) are defined in "loplsaa2023.lt",
   #    @atom:54L     "C - CT | n-CH3 C: alkane (LOPLS, 2012)"
   #    @atom:57L     "C - CT | CH2 C: alkanes (LOPLS, 2012)"
   #    @atom:60LCH3  "H - HC | CH3 H: alkanes (LOPLS,2012)"
   #    @atom:60LCH2  "H - HC | CH2 H: alkanes (LOPLS,2012)"
   # In this example, atomic charges are generated by atom type (according to the
-  # rules in loplsaa.lt), and can be omitted. Just leave them as "0.0" for now.
+  # rules in loplsaa2023.lt), and can be omitted. Just leave them as "0.0" for now.
   # The "..." in "$mol:..." tells moltemplate that this molecule may be part
   # of a larger molecule, and (if so) to use the larger parent object's 
   # molecule id number as it's own.

examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3.lt

@@ -4,15 +4,15 @@
 # This file is located in the "force_fields" subdirectory
 # distributed with moltemplate.
 
-import "loplsaa.lt"   # <-- defines the standard "OPLSAA" force field as well as
+import "loplsaa2023.lt"   # <-- defines the standard "OPLSAA" force field as well as
                       #     custom parameters for long alkane chains taken from
                       #     Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 
 		      #     To use the ordinary OPLSAA force field parameters,
 		      #     (instead of the Sui et al. parameters), change the
 		      #     atom types below from "@atom:54L","@atom:60LCH3" to
-		      #     "@atom:54" and "@atom:60"  (defined in "oplsaa.lt")
+		      #     "@atom:54" and "@atom:60"  (defined in "oplsaa2023.lt")
 
-# The "loplsaa.lt" and "oplsaa.lt" files are located at:
+# The "loplsaa2023.lt" and "oplsaa2023.lt" files are located at:
 # https://github.com/jewettaij/moltemplate/tree/master/moltemplate/force_fields/
 # If you want to customize these files, download them and copy them to this folder.
 
@@ -36,13 +36,13 @@ CH3 inherits OPLSAA {
     $bond:ch3 $atom:c $atom:H3
   }
 
-  # Atom type numbers (@atom:54L,@atom:60LCH3) are defined in "loplsaa.lt",
+  # Atom type numbers (@atom:54L,@atom:60LCH3) are defined in "loplsaa2023.lt",
   #    @atom:54L     "C - CT | n-CH3 C: alkane (LOPLS, 2012)"
   #    @atom:57L     "C - CT | CH2 C: alkanes (LOPLS, 2012)"
   #    @atom:60LCH3  "H - HC | CH3 H: alkanes (LOPLS,2012)"
   #    @atom:60LCH2  "H - HC | CH2 H: alkanes (LOPLS,2012)"
   # In this example, atomic charges are generated by atom type (according to the
-  # rules in loplsaa.lt), and can be omitted. Just leave them as "0.0" for now.
+  # rules in loplsaa2023.lt), and can be omitted. Just leave them as "0.0" for now.
   # The "..." in "$mol:..." tells moltemplate that this molecule may be part
   # of a larger molecule, and (if so) to use the larger parent object's 
   # molecule id number as it's own.

examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/README.md

@@ -21,7 +21,7 @@ The number of molecules, positions, and simulation box size can be controlled by
 
 In this example, atomic charge for OPLSAA atoms is determined by @atom type
 *(...according to a lookup table located at the beginning of the
-["oplsaa.lt"](../../../moltemplate/force_fields/oplsaa.lt) file)*.
+["oplsaa2023.lt"](../../../moltemplate/force_fields/oplsaa2023.lt) file)*.
 *(Any atomic charges listed in the "Data Atoms" section of your molecules'
 LT files will be ignored.)*
 **These charges can be overridden.**