MBO(N)D: A multibody method for long-time molecular dynamics simulations

✍ Scribed by Chun, Hon M.; Padilla, Carlos E.; Chin, Donovan N.; Watanabe, Masakatsu; Karlov, Valeri I.; Alper, Howard E.; Soosaar, Keto; Blair, Kim B.; Becker, Oren M.; Caves, Leo S. D.; Nagle, Robert; Haney, David N.; Farmer, Barry L.

• Publisher: John Wiley and Sons
• Year: 2000
• Tongue: English
• Weight: 706 KB
• Volume: 21
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(200002)21:3<159::aid-jcc1>3.0.co;2-j

✦ Synopsis

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also