Discrete molecular dynamics

作者：Proctor Elizabeth A; Ding Feng; Dokholyan Nikolay V^*

来源：Wiley Interdisciplinary Reviews: Computational Molecular Science , 2011, 1(1): 80-92.

DOI：10.1002/wcms.4

Discrete molecular dynamics (DMD) has emerged as a simplification of traditional molecular dynamics (MD). DMD employs discrete step function potentials in place of the continuous potential used in traditional MD. As a result, the simulation engine solves the ballistic equations of motion for only those particles participating in a collision, instead of solving Newton's equations of motion for every particle in the system. Because fewer calculations are performed per time step, the DMD technique allows for longer time and length scales to become accessible in the simulation of large biomolecules. The use of coarse-grained models extends the computational advantage of this method. Although some accuracy is sacrificed to speed, because of the usefulness of DMD to the simulation of many particles at longer timescales, the technique has seen application to diverse molecular systems.

• 出版日期2011-2