Effect of Center-of-Mass Motion Removal in the Molecular Dynamics Simulations
WAN Rong-Zheng1, LI Song-Yan1, FANG Hai-Ping1,2
1Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800 2Theoretical Physics Center for Science Facilities (TPCSF), Chinese Academy of Sciences, Beijing 100049
Effect of Center-of-Mass Motion Removal in the Molecular Dynamics Simulations
WAN Rong-Zheng1, LI Song-Yan1, FANG Hai-Ping1,2
1Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800 2Theoretical Physics Center for Science Facilities (TPCSF), Chinese Academy of Sciences, Beijing 100049
Molecule dynamics simulation is now widely used in the study of nano pores, proteins and nano-scale devices. The limited friction in such a system requires the method of center-of-mass motion removal to be applied. We test the effect of different time period T of this method under osmotic pressure difference, and find that the impact on the net flux is very small together with the effective reduction of the accumulated numerical error when the period T is above 0.1 ps. The simulation results also show that the change of this time period of method has very little effect on the potential of mean force of the water inside the carbon nanotubes.
Molecule dynamics simulation is now widely used in the study of nano pores, proteins and nano-scale devices. The limited friction in such a system requires the method of center-of-mass motion removal to be applied. We test the effect of different time period T of this method under osmotic pressure difference, and find that the impact on the net flux is very small together with the effective reduction of the accumulated numerical error when the period T is above 0.1 ps. The simulation results also show that the change of this time period of method has very little effect on the potential of mean force of the water inside the carbon nanotubes.
WAN Rong-Zheng;LI Song-Yan;FANG Hai-Ping;. Effect of Center-of-Mass Motion Removal in the Molecular Dynamics Simulations[J]. 中国物理快报, 2010, 27(8): 84702-084702.
WAN Rong-Zheng, LI Song-Yan, FANG Hai-Ping,. Effect of Center-of-Mass Motion Removal in the Molecular Dynamics Simulations. Chin. Phys. Lett., 2010, 27(8): 84702-084702.
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