Initial commit
Initial commit of Emilio's provided code
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Add amber files.
Update all to latest versions
Fixed the date script with help from Emilio. _LaunchReplicas was setting the member data rather than returning a value as was expected in pj_sync_re.py.
General clean-up of the code Emilio and I write originally.
The code now allows for multi-dimensional biases by using colon separated lists of force constants and bias positions. The restraint template file now has to have dummy values with an additional dimension index (even if using 1 dimension). However everything will still work fine if you don't have colons in the configuration file.

TODO: - Run in parallel
      - Take AMBER groupfiles for initial coordinates, etc.?
A sander executable is now assumed (should probably expand the ENGINE flag to change this), and a serial or parallel executable will be looked for depending on whether SPMD = 'single' or 'mpi'. I don't know how stable this is, but it seems to work on my desktop.
AMBER now runs on my workstation and XSEDE (Lonestar) with MPI executables. I have not scaled this beyond 4 jobs on 1 node yet...
Changed Amber's launchReplica to use the pilot (faster than data service)
Added setup.py installation script
Implemented RE Gibbs sampling for BEDAM (experimental)
Introduced SUBJOBS_BUFFER_SIZE variable.

It's the number of waiting subjobs maintained in the bigjob queue
specified as a fraction of the number of slots. For example if each
replica uses 4 cores of a 384-cores job (96 replicas running), specifing:
SUBJOBS_BUFFER_SIZE=0.5
will hold approximately 48 replicas in the waiting queue.
Added "bliss" dependency
Impact/BEDAM examples
Added installation instructions
Added a MANIFEST file to include examples in distribution
Added a hack flag to amberus_async_re to turn off exchanges in the case that one wants to run simple equilibration runs (although I'm not even sure this is necessary, will have to experiment).

Added a serial test of AMBER/sander running 2d umbrella sampling. I have not fully tested the mpi implementation (that will need to be done on XSEDE) and have not touched AMBER/pmemd at all yet since we have no immediate plans to use that.
There was a logical bug in pj_async_re whereby the value of the SPMD flag was ignored. If it existed then it was automatically set to "mpi" and if not it was set to "single". This is now changed and the default behavior now depends on the value of PPN, which defaults to 1 (spmd = "single"). ppn < 0 now exits.

The AMBER code now checks for which MD engine is desired (sander or pmemd) and accepts multiple designations. The old expected flag of "AMBER" defaults to sander, since pmemd has lower functionality. There is still no catch for pmemd (or sander) bombing on bad input options.

I also cleaned up some of the input checking, although I'm not sure this is done entirely properly in the inheritance scheme...