I've installed and compiled updated versions of NAMD and VMD on Cyrus1. I'll do the same on Quantum2 this weekend if I can. The following binaries can be found in /usr/group on cyrus1:
catdcd charmrun flipbinpdb flipdcd namd2 psfgen vmd (vmd is technically not a binary)
Users can specify the fulll location or modify their paths, as they see fit. Please note that I copied this directory to all the compute nodes.
More details:
Charm++ 6.2: compiled against OpenMPI, in /usr/src/charm-6.2.0/mpi-linux-x86_64-mpicxx/
NAMD 2.7b2: compiled from source using Charm++ 6.2, in /usr/src/NAMD_2.7b2_Source/Linux-x86_64-g++
VMD 1.8.7: /usr/src/vmd-1.8.7, binary downloaded.
catDCD 4.0
Other users who have installed software should feel free to follow this same model, placing source code in the /usr/src directory and executables in the /usr/group directory.