THIS IS A READ-ONLY REPOSITORY. SMOG-CHECK IS NOW BUNDLED
WITH SMOG2.


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README for smog-check version 2.5beta. These are very simple 
scripts that will test to see if your installation of SMOG 2 
is generating CA, CA-CB and AA .top files that are consistent 
with the default settings. They also check to see if the 
model parameters can be adjusted properly.

smog-check is free software, distributed under the GNU
General Public License. See COPYING.

            Paul Whitford, Jeffrey Noel

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			USAGE

There are three check scripts provided by this bundle: 
checkall
smog-check
scm-check
smog-tool-check

When everything works well, running the checks is 
fairly quick and easy.  Just make sure you run 
configure.smog2 for the version of SMOG 2 that you would
like to test, and make sure SMOG 2 is in your path.
If all is well, then you can run all tests with the single
command:

>./checkall

If everything passes, you are done.  No need to read further.

If you prefer, you can run the tests individually, as described
below.


                  SMOG CHECK

From the smog-check directory, issue the command:

./smog-check 

If you would like to only perform a specific test, you
can indicate which test with

./smog-check N

where N is the test you would like to repeat.  This can 
be useful when debugging SMOG 2.

If you would like to only perform tests N to M, indicate 
which tests with

./smog-check N M

You can also optionally verify that the generated top/gro
files can be processed by gromacs 4, or gromacs 5. This is generally
not needed, and it can be very slow (hours). However, if you are modifying
SMOG 2, then it can be helpful to verify that everything is formatted
in a manner that is consistent with gromacs. Indicating
which versions of gromacs to use is accomplished by exporting the following
environment variables:
GMXVER : set to 4 or 5 to indicate which version of gromacs will be used
CHECKGMX : set to "yes" to turn on compatibility check with grompp
GMXPATH : path to the gromacs executable
CHECKGMXGAUSSIAN : set to "yes" to also check gaussian-based files
GMXPATHGAUSSIAN : path to the gromacs executable for gromacs-based files
Note: GMX checks may also be enabled when using smog-tool-check

                  TOOL CHECK

To check that the smog tools are working properly, use:

./smog-tool-check

smog-tool-check is not very comprehensive, but it will 
ensure basic functionality of the tools.

If you would like to only test some tools, then indicate
the tools to test on the command line.  For example, if
you want to test smog_ions, only, then call

./smog-tool-check ions

These scripts have been tested on Linux and OSX 
platforms. 

                  SCM CHECK

If you plan to use the Shadow Contact Map software (SCM.jar) 
as a standalone application, then you can test it is working 
with scm-check


Direct all questions and suggestions to info@smog-server.org.

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