Molmodel 2.2 Examples README
                             June, 2011

This is a set of examples covering a range of systems that can be modeled 
with Molmodel, including proteins and RNA.

Precompiled binaries of these programs are installed in the 
examples/molmodel/bin directory. In particular, you can run 
MolmodelInstallTest to check installation, or MolmodelInstallTestNoViz to 
check that everything other than the Visualizer is working. You should be 
able to re-create these binaries using the source provided here and 
instructions below.

We have supplied an example Makefile that will work on Linux and Mac, and
a CMakeLists.txt file that will work on all platforms. Although we have not
provided a pre-built Visual Studio solution file, CMake will quickly 
create one for you from the CMakeLists.txt and we strongly recommend that
approach. If you don't have it already, go to cmake.org and download 
CMake 2.8 or later. Then run the CMake GUI, tell it the source directory 
(where it will look for CMakeLists.txt) hit "Configure", tell it what 
compiler you want to use, then hit "Generate" and exit. You will then 
have a nice Visual Studio solution (.sln) file you can click on. This 
should also work for building an XCode project on the Mac although we 
haven't tested that yet. And CMake also creates ordinary make files like 
the one supplied here.

The CMakeLists.txt file here creates a single build environment containing 
separate projects for each of the examples. That works on all platforms, 
using whatever build system is appropriate.

If you want to make your own Visual Studio solution by hand, see 
README_VisualStudio.txt.

If you want to use the supplied Makefile: see README_Makefile.txt.


General Instructions
--------------------
Download CMake 2.8 or later from http://www.cmake.org. Be sure to tell 
CMake to use the version of the compiler that you intend to use. Note 
that you must use a version that is compatible with the installed 
Simbody and Molmodel binaries. If you can't find a suitable pre-built binary
for your compiler you'll have to build the Molmodel library from the source
distribution. That's not very hard -- see the step-by-step instructions.

There are platform dependencies regarding running CMake; basically either
click on the icon (Windows) or run the ccmake UI. Make sure it understands
where Simbody and Molmodel were installed (it should see the 
SimTK_INSTALL_DIR environment variable).

For help, post to the Molmodel project help Forum, at 
https://simtk.org/home/molmodel, Advanced tab, Public Forums.


Special Instructions
--------------------

ExampleAdenylateMobilitiesVMD

There are special instructions for running ExampleAdenylateMobilitiesVMD
because you have to install and run VMD for displaying the results. See
ExampleAdenylateMobilitiesVMD_Notes.txt.

ExampleLoadPdb[2]

The two ExampleLoadPdb examples expect to find their pdb files in the
current directory. If you are running them from somewhere other than
the Examples source directory, copy the pdb files there.