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} |
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|
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
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|
atom types (transition metals, point dipoles, sticky potentials, |