# -------- WARNING: --------

This directory contains some examples of all-atom simulations using the COMPASS
force field.

This software is experimental, and the force-fields and equilbration protocols
have not been tested carefully by me.  There is no gaurantee that simulations
prepared using moltemplate will reproduce the behavior of other MD codes.

The moltemplate implementation of COMPASS currently relies on the same
incomplete force-field file that "msi2lmp" uses ("compass_published.frc").
Unfortunately this means that many force field parameters and some atom types
(such as sp2-carbons) have not (yet) been publicly released and are not
available.

Currently I recommend that users should run the "cleanup_moltemplate.sh"
script after running "moltemplate.sh system.lt".  Then manually check that 
the "system.in.settings" and "system.in.charges" files which remain 
make sense.  Specifically, you must check that the angle_coeff,
dihedral_coeff, bond_coeff commands are not full of zeros (in places
where they should not be zero.  This is another consequence of the
fact that the .FRC files I mentioned above are incomplete.)  It's a
good idea to also check that the charges in the "system.in.charges"
file seem reasonable (ie. not all zeros).  (There is a list of
warnings at the end of the "compass_published.lt" file.  You can check
to see if any of the bonds in your system are covered by these
warnings.)  Later on hopefully I'll add some automated way to warn
users when these problems arise, but now you should check for them
manually.

# -------- REQUEST FOR HELP: --------

If you notice a problem with these examples, please report it.
Peer-review is the only way to improve this software (or any software).
Other suggestions are also welcome!

(Contact jewett.aij@gmail.com, 2017-10-03)

