Java based high-performance generic molecular dynamics simulation code supporting standard gromacs input files

Parallel computing algorithm is implemented using MPJ-Express library(http://mpj-express.org), and Particle-Mesh-Ewald summation for fast long-range interaction requires FFT library provided by JTransforms(https://sites.google.com/site/piotrwendykier/software/jtransforms).

To run a regular MD simulation on a single core machine.

RunSkeleton [prm file] [gro file] [top file] [out traj] [out energy]

To run a regular MD simulation on a distributed memory multi-core/multi-node machone.

mpjrun.sh -np [number of cores] MpiRunSkeleton [prm file] [gro file] [top file] [out traj] [out energy]

parallel computation on a distrubted memory system(e.g. cluster computer) is supported through MPJ express library. Current version supports domain-based decomposition which results in better scaling performance compared to particle-based decomposition.

can use standard Gromacs like input files (e.g. *.gro, *.itp, *.top) allowing one to use this code to complement package programs.

unlike package programs, myMD code is developed as a flexible tool to suit various different types of simulations. Document explaining full API will be provided in the near future.