addressed the concerns of issue #98 (confusing example explanation)

examples/all_atom/force_field_AMBER/hexadecane/run.in.npt

@@ -19,7 +19,16 @@ include         system.in.settings
 
 # ------------------------------- Run Section -------------------------------
 
-# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, 
+# Explanation.
+# Unless you use packmol (or some other geometry generation program),
+# the initial geometry created by moltemplate using a lattice is
+# extremely unrealistic for a liquid, and likely to put the system
+# a kinetic trap (local minimum). So this example uses high temperatures
+# to completely obliterate any memory of that initial lattice shape.
+# Then it uses a combination of high pressures and cooling to bring
+# the system back down to a temperature and density of a liquid at 1atm, 300K.
+
+# I am using a 4-step equilibraion process (expand, minimize,
 # reorient, compress).  The system (as defined in the "system.data" file) 
 # is already expanded.  That means there are 3 steps left:
 

examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt

@@ -20,7 +20,16 @@ include         system.in.charges
 
 # ------------------------------- Run Section -------------------------------
 
-# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, 
+# Explanation.
+# Unless you use packmol (or some other geometry generation program),
+# the initial geometry created by moltemplate using a lattice is
+# extremely unrealistic for a liquid, and likely to put the system
+# a kinetic trap (local minimum). So this example uses high temperatures
+# to completely obliterate any memory of that initial lattice shape.
+# Then it uses a combination of high pressures and cooling to bring
+# the system back down to a temperature and density of a liquid at 1atm, 300K.
+
+# I am using a 4-step equilibraion process (expand, minimize,
 # reorient, compress).  The system (as defined in the "system.data" file) 
 # is already expanded.  That means there are 3 steps left:
 

examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt

@@ -20,7 +20,16 @@ include         system.in.charges
 
 # ------------------------------- Run Section -------------------------------
 
-# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, 
+# Explanation.
+# Unless you use packmol (or some other geometry generation program),
+# the initial geometry created by moltemplate using a lattice is
+# extremely unrealistic for a liquid, and likely to put the system
+# a kinetic trap (local minimum). So this example uses high temperatures
+# to completely obliterate any memory of that initial lattice shape.
+# Then it uses a combination of high pressures and cooling to bring
+# the system back down to a temperature and density of a liquid at 1atm, 300K.
+
+# I am using a 4-step equilibraion process (expand, minimize,
 # reorient, compress).  The system (as defined in the "system.data" file) 
 # is already expanded.  That means there are 3 steps left:
 
@@ -49,7 +58,7 @@ dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy
 # using fix langevin (and fix nve).  Then I switch to fix nvt (Nose-Hoover).
 # (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.)
 
-# Give each atom a random initial velocity consistent with a system at 300K.
+# Give each atom a random initial velocity consistent with a system at 900K.
 velocity all create 900.0 12345
 
 # Run a short simulation using a Langevin thermostat.