it makes sure that transitions such as i j -> i k are taken into account and writes downs all the four anchors involved in the transition, also the output.PTH will write all the final configurations

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5016 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Added documentation about variables

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5021 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed linking of CUDA binary in CMakeLists.txt


git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5035 90e2fc84-bd37-0410-82f1-ae2f889bfac2
code to create binary solutions of water and cosolvent

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5036 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Added Mauro L. Mugnai's presentation on the inner workings of MUTA to the repository.


git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5039 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Generate code for multiple GPU architectures in the same binary.


git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5042 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed bug with allocation of 1-4 interactions (now it's in the main branch too)


git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5043 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed bug involving mismatches between hardcoded masses for water atoms and the corresponding masses coming from connectivity files.  These discrepancies were causing problems in mshake.


git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@5044 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Direct space Lennard-Jones 6 contributions.
PME6 working.
Merge branch 'master' of github.com:jmbr/moil