Reenabled output of energy of bonded interactions.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4885 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed permissions in dyna14 source code.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4886 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Removed stale PME C++ code.  This is part of an ongoing effort to get rid of compiler warnings.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4887 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Progress towards reenabling torsion constraints for DIM.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4888 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Further amendments.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4889 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Merge branch 'master' of github.com:jmbr/moil
Merge branch 'master' of github.com:jmbr/moil