This is a simple system of 826 water molecules.

In this example, the coordinates of the atoms are read from a PDB file
instead of being specified manually (as well as the boundary information).

The PDB file was generated by the useful "solvate" utility which comes with VMD.
(To generate this file yourself, run VMD, click on the "Extensions" menu, 
and select Modeling-->Add Solvation Box.
In this example, I made a box whose x,y,z dimensions were 30.0,30.0,30.0.)

Although I based the water model on SPC/E water model,
it differs from that model in several important ways:
Unlike the real SPC/E model,
the water model used in this example is NOT rigid,
and I did NOT use long-range electrostatics.
If anyone would like to improve this example please contact me
or submit a pull-request on github.
(Links to both are online http://www.moltemplate.org/espresso)
Details on the SPC/E water model can be found here:
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987)



---- Reading coordinates from an external file (PDB file) ----

You must tell emoltemplate to look for the coordinates in a separate file
using the "-pdb file.pdb" argument.  For example:

emoltemplate.sh -pdb solvate.pdb system.et

emoltemplate.sh will generate a file "system.tcl" containg TWO different
lists of coordinates. The first list contains coordinates, mass and charge

part 0    pos 0.0 0.0 0.0 type 0 q -0.8476 mass 16.0
part 1    pos 0.81649 0.577359 0.0 type 1 q 0.4238 mass 1.0
part 2    pos -0.81649 0.577359 0.0 type 1 q 0.4238 mass 1.0
     :
part 2477 pos -0.81649 0.577359 0.0 type 1 q 0.4238 mass 1.0

      These coordinates are incorrect, but the mass and charge are correct.
      The second list contains only coordinate information.  The coordinates in
      this second list come from the PDB file, and (hopefully) should override
      the coordinates in the first list.  (I have not tested this.
      Hopefully ESPRESSO does not mind if we specify the coordinates twice.)

part 0    pos 3.668 10.082 15.904
part 1    pos 3.224 10.451 15.101
part 2    pos 3.092 10.379 16.627
     :
part 2477 pos 4.264 10.639 19.456

