| FUNDAMENTAL AREAS OF PHENOMENOLOGY(INCLUDING APPLICATIONS) |
|
|
|
|
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 |
|
| Cite this article: |
|
WAN Rong-Zheng, LI Song-Yan, FANG Hai-Ping 2010 Chin. Phys. Lett. 27 084702 |
|
|
|
|
Abstract 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.
|
| Keywords:
47.11.Mn
87.15.Ap
|
|
|
Received: 26 March 2010
Published: 28 July 2010
|
|
| PACS: |
47.11.Mn
|
(Molecular dynamics methods)
|
| |
87.15.ap
|
(Molecular dynamics simulation)
|
|
|
|
|
|
[1] Hummer G, Rasaiah J C and Noworyta J P 2001 Nature 414 188
[2] Kalra A et al 2003 Proc. Natl. Acad. Sci. U.S.A. 100 10175
[3] Waghe A, Rasaiah J C and Hummer G 2002 J. Chem. Phys. 117 10789
[4] Berezhkovskii A and Hummer G 2002 Phys. Rev. Lett. 89 064503
[5] Wan R Z, Li J Y, Lu H J and Fang H P 2005 J. Am. Chem. Soc. 127 7166
[6] Li J Y et al 2007 Proc. Natl. Acad. Sci. U.S.A. 104 3687
[7] Wan R Z, Lu H J, Li J Y, Bao J D, Hu J and Fang H P 2009 Phys. Chem. Chem. Phys. 11 9898
[8] Gong X J et al 2007 Nature Nanotechnol. 2 709
[9] Zhu F Q, Tajkhorshid E and Schulten K 2004 Biophys. J. 86 50
[10] Zhu F Q, Tajkhorshid E and Schulten K 2002 Biophys. J. 83 154
[11] Anishkin A and Sukharev S 2004 Biophys. J. 86 2883
[12] Berne B J, Weeks J D and Zhou R H 2009 Annu. Rev. Phys. Chem. 60 85
[13] Wang Y and Yuan H J 2007 Chin. Phys. Lett. 24 3276
[14] Xiu P et al 2009 J. Am. Chem. Soc. 131 2840
[15] Wang C L et al 2009 Phys. Rev. Lett. 103 137801
[16] Lindahl E, Hess B and Spoel D 2001 J. Mol. Model 7 306
[17] Sun L and Crooks R M 2000 J. Am. Chem. Soc. 122 12340
[18] Bourlon B et al 2006 Nature Nanotechnol. 2 104
[19] Zheng M et al 2003 Nature Mater. 2 338
[20] Ajayan P M et al 1995 Nature 375 564
[21] Thomas J A and McGaughey A J H 2009 Phys. Rev. Lett. 102 184502
[22] Jensen MØPark S, Tajkhorshid E, and Schulten K 2002 Proc. Natl. Acad. Sci. U.S.A. 99 6731
[23] Liu J et al 1998 Science 280 1253
[24] Brenner D W 1990 Phys. Rev. B 42 9458
[25] Tersoff J 1988 Phys. Rev. Lett. 61 2879
[26] Jorgensen W L et al 1983 J. Chem. Phys. 79 926
[27] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
[28] Mann D J and Hall M D 2003 Phys. Rev. Lett. 90 195503
[29] Pomés R and Roux B 1998 Biophys. J. 75 33
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
