TODO

Critical Path (NSF Objectives)

    Flexibility                   Finish by December 2016
    ↙         ↘
Solutes    Step Parallelism       Finish by May 2017
   ↓
 QM/MM                            Finish by August 2017

Chemistry/Major Functionality

• Support molecule flexibility (In progress: Brandon Su16, Mitch Fa16)
• Implement/find code for NLC on CPU
• Integrate Verlet on CPU (from branch)
• Parallelize NLC on GPU
• Parallelize Verlet on GPU
• Support NPT ensembles
• Quadratic feathering
• Ewald summations
• Step parallelism
• Free energy perturbation calculations
• Solutes
• QM/MM

Design, Cleanup, and Documentation

• Update Makefile to compile with GCC without OpenACC (CPU-only/no GPU)
• Add tests from Orlando's 5/26 e-mail
• Refactor Simulation/SimBox/etc. design per 5/26 discussion
  • Fix CLI args to accommodate varying cutoff methods (brute-force, matrix, NLC, Verlet)
  • Add testing capabilities for new calculation strategies
• Update Makefile to compile with PGCC with -ta=multicore (In progress: Brandon)
• Update Makefile to compile with GCC with OpenACC

Inessential

• Zmat explicit conversion script - add implicit angles to Z-matrix file