384405 The Need for New Tools to Explore Hypothetical Molecular Systems
Dramatic increases in computer power combined with steady improvements in simulation algorithms have significantly reduced a key bottleneck in modeling large, complex molecular systems: hardware costs. However, the waning of the hardware cost bottleneck has revealed other bottlenecks that were not previously apparent. For small systems humans have been able to manually construct trial molecular configurations (i.e, choosing initial coordinates for a handful of atoms in a small molecule) and then relax their structures (or observe their time evolution) using various simulation methods. However, for systems involving thousands of atoms creating trial configurations is much more challenging. Whereas in the case of modeling naturally occurring or already experimentally synthesized systems one can obtain reasonable trial coordinates from x-ray crystallography (or analogous measurement techniques), this is not possible for large hypothetical systems. Since it is, in principle, a fundamental strength of molecular simulations to be able to explore hypotheses in advance of comparatively much more expensive experiments, the inability to efficiently generate trial coordinates for large hypothetical systems is a painful constraint.
Certain tools, such as Packmol , which generate trial coordinates for tightly packed molecules in user-defined volumes partially address this need, but in this presentation I will discuss other challenges that have yet to be addressed. Analogies to tools developed in mechanical engineering, architecture, and computer graphics will be discussed, and I will explore the idea that there is significant room for innovation in designing new tools for exploring hypothetical molecular systems.
 L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez. Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13):2157-2164, 2009.
See more of this Group/Topical: Computational Molecular Science and Engineering Forum