Many biological processes are characterized by an essentially quantum dynamical event, such as electron or proton transfer, in a complex classical environment. To treat such processes properly by computer simulation, allowing nonadiabatic transitions involving excited states, we recently developed a
Hybrid molecular dynamics: an approach to low density simulations
✍ Scribed by Mark S.C. Reed; K.M. Flurchick
- Publisher
- Elsevier Science
- Year
- 1994
- Tongue
- English
- Weight
- 727 KB
- Volume
- 81
- Category
- Article
- ISSN
- 0010-4655
No coin nor oath required. For personal study only.
✦ Synopsis
A new molecular dynamics technique is described which addresses the special problems intrinsic to low density simulations, particularly fluids in the gas phase. This technique incorporates aspects of both the conventional hard spheres and continuous potential molecular dynamics algorithms. The difficulties inherent in low density simulations are discussed and the synthesis of existing molecular dynamics techniques into a new, hybrid algorithm is described in detail, including optimization and vectorization modifications. Finally, benchmarks for the new code are reported which show a speedup of up to a factor of 7 over a traditional molecular dynamics program.
📜 SIMILAR VOLUMES
## Abstract To investigate the solvation structure of the Cu^ii^ ion in liquid ammonia, ab initio quantum‐mechanical/molecular‐mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold‐coordinated spe
## Abstract RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the a
The temperature dependence of atomic and electronic structures in liquid Se 30 Te 70 is studied using ab initio molecular dynamics simulations. Our work verifies the structural change from low-to highdensity phases observed in experiments. Moreover, we show that the structure of low-density liquid i