Added VM preparation script

tools/setup_centos_vm.sh

+# Prepare a vagrant CentOS 6.5 VM for building OpenMM
+# Needs latest version of vagrant to auto-download the chef package
+#vagrant init chef/centos-6.5
+#vagrant up
+#vagrant ssh
+
+
+# Download and enable the EPEL RedHat EL extras repository
+mkdir Software
+cd Software
+sudo yum install wget -y
+wget http://mirror.umd.edu/fedora/epel/6/i386/epel-release-6-8.noarch.rpm
+sudo rpm -i epel-release-6-8.noarch.rpm
+
+sudo yum update
+
+# Several of these come from the EPEL repo
+sudo yum install clang-3.4 cmake28 graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim -y
+
+# Probably can't use RHEL6 version of doxygen because it's very old.
+wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.7.src.tar.gz
+rpmbuild -ta doxygen-1.8.7.src.tar.gz
+sudo rpm -i ~/rpmbuild/RPMS/x86_64/doxygen-1.8.7-1.x86_64.rpm
+
+# Install CUDA6 for RHEL6
+cd ~/Software
+wget http://developer.download.nvidia.com/compute/cuda/repos/rhel6/x86_64/cuda-repo-rhel6-6.0-37.x86_64.rpm
+sudo rpm -i  cuda-repo-rhel6-6.0-37.x86_64.rpm
+sudo yum clean expire-cache
+sudo yum install cuda -y
+
+
+# Download AMD APP SDK from here, requires click agreement: http://developer.amd.com/amd-license-agreement-appsdk/
+mkdir ~/AMD
+cd ~/AMD
+# Copy the tarball to this directory from wherever you got it.
+cp /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz  ./
+tar -zxvf  /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz
+
+cd ~/Software
+wget http://repo.continuum.io/miniconda/Miniconda-3.0.5-Linux-x86_64.sh
+bash Miniconda-3.0.5-Linux-x86_64.sh -b
+
+export PATH=$HOME/miniconda/bin:$PATH
+
+
+
+# MANUAL installation below this point###
+# MANUAL installation below this point###
+# MANUAL installation below this point###
+
+conda config --add channels http://conda.binstar.org/omnia
+conda install --yes fftw3f jinja2 swig sphinx conda-build
+
+#git clone https://github.com/SimTk/openmm.git
+git clone -b vagrant https://github.com/kyleabeauchamp/openmm.git
+cd openmm
+conda install --file tools/ci/requirements-conda.txt --yes
+export CC="clang++"
+conda build tools/conda-recipe