TY - JOUR
T1 - The neighbor list algorithm for a parallelepiped box in molecular dynamics simulations
AU - Cui, Zhiwei
AU - Sun, Yi
AU - Qu, Jianmin
PY - 2009/5
Y1 - 2009/5
N2 - In classic molecular dynamics (MD) simulations, the conventional Verlet table, cell linked list and many other techniques have been adopted to increase the computational efficiency. However, these methods are only applicable in cubic systems. In this work, the above techniques along with the metric-tensor method are extended to handle NP ensembles, so that MD simulations can be carried out under the most general loading conditions. In order to do so, a particular spatial Cartesian reference frame is proposed to determine the scaling matrix. Also, a combination method, taking the advantages of the improved Verlet table and cell linked list, is established to identify the neighbor atoms very quickly in a parallelepiped box. An example using Lennard-Jones potential is presented to verify the validity of the proposed algorithm.
AB - In classic molecular dynamics (MD) simulations, the conventional Verlet table, cell linked list and many other techniques have been adopted to increase the computational efficiency. However, these methods are only applicable in cubic systems. In this work, the above techniques along with the metric-tensor method are extended to handle NP ensembles, so that MD simulations can be carried out under the most general loading conditions. In order to do so, a particular spatial Cartesian reference frame is proposed to determine the scaling matrix. Also, a combination method, taking the advantages of the improved Verlet table and cell linked list, is established to identify the neighbor atoms very quickly in a parallelepiped box. An example using Lennard-Jones potential is presented to verify the validity of the proposed algorithm.
KW - Molecular dynamics simulations
KW - Neighbor algorithm
KW - Parallelepiped box
UR - http://www.scopus.com/inward/record.url?scp=65649149028&partnerID=8YFLogxK
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U2 - 10.1007/s11434-009-0197-0
DO - 10.1007/s11434-009-0197-0
M3 - Article
AN - SCOPUS:65649149028
SN - 1001-6538
VL - 54
SP - 1463
EP - 1469
JO - Chinese Science Bulletin
JF - Chinese Science Bulletin
IS - 9
ER -