| 3 |
|
|
| 4 |
|
Absence of applying modern software development practices is the |
| 5 |
|
bottleneck of Scientific Computing community\cite{Wilson2006}. In |
| 6 |
< |
the last 20 years , there are quite a few MD packages that were |
| 7 |
< |
developed to solve common MD problems and perform robust simulations |
| 8 |
< |
. However, many of the codes are legacy programs that are either |
| 9 |
< |
poorly organized or extremely complex. Usually, these packages were |
| 10 |
< |
contributed by scientists without official computer science |
| 11 |
< |
training. The development of most MD applications are lack of strong |
| 12 |
< |
coordination to enforce design and programming guidelines. Moreover, |
| 13 |
< |
most MD programs also suffer from missing design and implement |
| 14 |
< |
documents which is crucial to the maintenance and extensibility. |
| 15 |
< |
Along the way of studying structural and dynamic processes in |
| 16 |
< |
condensed phase systems like biological membranes and nanoparticles, |
| 17 |
< |
we developed and maintained an Object-Oriented Parallel Simulation |
| 18 |
< |
Engine ({\sc OOPSE}). This new molecular dynamics package has some |
| 19 |
< |
unique features |
| 6 |
> |
the last 20 years , there are quite a few MD |
| 7 |
> |
packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed |
| 8 |
> |
to solve common MD problems and perform robust simulations . |
| 9 |
> |
Unfortunately, most of them are commercial programs that are either |
| 10 |
> |
poorly written or extremely complicate. Consequently, it prevents |
| 11 |
> |
the researchers to reuse or extend those packages to do cutting-edge |
| 12 |
> |
research effectively. Along the way of studying structural and |
| 13 |
> |
dynamic processes in condensed phase systems like biological |
| 14 |
> |
membranes and nanoparticles, we developed an open source |
| 15 |
> |
Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
| 16 |
> |
molecular dynamics package has some unique features |
| 17 |
|
\begin{enumerate} |
| 18 |
|
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
| 19 |
|
atom types (transition metals, point dipoles, sticky potentials, |
