Renamed MDP files with more descriptive names
Updated MDP files for energy minimization

Also updated setup script:
- Changed name of MDP file
- Automatically creates symlinks to MDP files in run directory
Updated MDP file for NVT run with fixed protein atoms

run/run_GROMACS_MD.bat
- Updated MDP file names
- Running across 2 nodes instead of 1 to exercise MPI
- Added '-j oe' option for automatically naming output files
- Un-commented NVT run

run/cleanup.sh
- Updated name of stdout and error files

run/setup_GROMACS_job.sh
- Reduced size of solvated box
- Fixed bug in find command that creates symlinks
    (added quotes to protect wildcards from shell expansion)
Updated MDP files for NPT constrained and NPT unconstrained

Changed options to match official tutorial more closely

Changes to run/run_GROMACS_MD.bat:
- Now allowing all GROMACS output to go to standard out, since redirection wasn't working
- Only MPI/Torque/Moab output goes to .out file
- Changed names of output files to clarify which output has constrained atoms