replaced rattle-->shake in the documentation. (I already changed it i…

…n the examples.)

doc/doc_mol22lt.md

@@ -271,7 +271,7 @@ Make sure they remain uniquely named, even after changing capitalization.)*
 
 ## Working with multiple chains
 
-As a workaround, if your MOL2 file contains multiple chains,
+If your MOL2 file contains multiple chains,
 split it into multiple MOL2 files (one per chain).
 Then convert each file separately.
 Afterwards, if you want to define a large molecular complex
@@ -281,8 +281,8 @@ multiple chain subunits.  For example, suppose we have a .mol2 file containing
 two chains. If we split that file into two files ("chainA.mol2", "chainB.mol2"),
 we can create two .lt files, one for each chain:
 ```
-mol22lt.py --in chainA.mol2 --out chainA.lt --name ChainA --ff GAFF2 --ff-file "gaff2.lt
-mol22lt.py --in chainB.mol2 --out chainB.lt --name ChainB --ff GAFF2 --ff-file "gaff2.lt
+mol22lt.py --in chainA.mol2 --out chainA.lt --name ChainA --ff GAFF2 --ff-file "gaff2.lt"
+mol22lt.py --in chainB.mol2 --out chainB.lt --name ChainB --ff GAFF2 --ff-file "gaff2.lt"
 ```
 Then we can then can manually create a new .lt file
 (eg. "protein_with_2_chains.lt")

doc/moltemplate_manual_src/moltemplate_manual.tex

@@ -1477,7 +1477,7 @@ \subsection{Simulating a box of water using moltemplate and LAMMPS}
    %combining this LT file with other LT files.)
 In addition to coordinates, topology and force-field settings, 
 ``LT'' files can optionally include any other kind of LAMMPS settings
-including RATTLE constraints, k-space settings, and even group definitions.
+including RATTLE or SHAKE constraints, k-space settings, and even group definitions.
   %\pagebreak
 \begin{verbatim}
 # (NOTE: Text following '#' characters are comments)
@@ -1544,8 +1544,8 @@ \subsection{Simulating a box of water using moltemplate and LAMMPS}
 
     # Group definitions and constraints can also go in the "In Settings" section
     group spce type  @atom:O  @atom:H
-    fix fRATTLE spce rattle 0.0001 10 100 b @bond:OH a @angle:HOH
-    # (lammps quirk: Remember to "unfix fRATTLE" during minimization.)
+    fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
+    # (lammps quirk: Remember to "unfix fSHAKE" during minimization.)
   }
 
   # LAMMPS supports a large number of force-field styles. We must select
@@ -3960,8 +3960,8 @@ \subsection{Mixing molecule types}
   # miscellaneous
   write_once("In Settings") {
     group spce type  @atom:O  @atom:H
-    fix fRATTLE spce rattle 0.0001 10 100 b @bond:OH a @angle:HOH
-    # (Remember to "unfix" fRATTLE during minimization.)
+    fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
+    # (Remember to "unfix" fSHAKE during minimization.)
   }
 
 } # SPCE