Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

Journal of Chemical Physics

Volumn 137, Issue 13, 2012, Pages

  Tao, Peng ^a   Wu, Xiongwu ^a   Brooks, Bernard R ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARTESIANS; INTEGRATION SCHEME; ITERATIVE PROCEDURES; MODEL SYSTEM; MOLECULAR DYNAMICS SIMULATIONS; NUMERICAL TESTS; RIGID BODY; ROTATION MATRICES; UNIQUE FEATURES;

ALGORITHMS; LAGRANGE MULTIPLIERS; MATRIX ALGEBRA; MOLECULAR DYNAMICS; NUMERICAL METHODS; RIGID STRUCTURES;

ITERATIVE METHODS;

PEPTIDE; PROTEIN; WATER;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MOLECULAR DYNAMICS;

ALGORITHMS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEINS; WATER;

EID: 84870212823     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4756796     Document Type: Article

References (20)

1. I. G. Tironi, R. M. Brunne, and W. F. van Gunsteren, Chem. Phys. Lett. 250, 19 (1996). 10.1016/0009-2614(95)01434-9
2. S. Karl, E. T. Robert, G. S. Bobby, and W. N. Donald, Nanotechnology 8, 103 (1997). 10.1088/0957-4484/8/3/002
3. A. V. Borisov and I. S. Mamaev, Regul. Chaotic Dyn. 7, 177 (2002). 10.1070/RD2002v007n02ABEH000204
4. J. B. Klauda, M. F. Roberts, A. G. Redfield, B. R. Brooks, and R. W. Pastor, Biophys. J. 94, 3074 (2008). 10.1529/biophysj.107.121806
5. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977). 10.1016/0021-9991(77)90098-5
6. H. C. Andersen, J. Comput. Phys. 52, 24 (1983). 10.1016/0021-9991(83) 90014-1
7. X.-W. Wu and S.-S. Sung, J. Comput. Chem. 19, 1555 (1998). 10.1002/(SICI)1096-987X(19981115)19:14<1555::AID-JCC13.0.CO;2-I
8. T. R. Forester and W. Smith, J. Comput. Chem. 19, 102 (1998). 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC93.0.CO;2-T
9. H. M. Chun, J. Comput. Chem. 21, 159 (2000). 10.1002/(SICI)1096- 987X(200002)21:3<159::AID-JCC13.0.CO;2-J
10. R. Kutteh and R. B. Jones, Phys. Rev. E 61, 3186 (2000). 10.1103/PhysRevE.61.3186
11. N. Neto and L. Bellucci, Chem. Phys. 328, 259 (2006). 10.1016/j.chemphys.2006.07.009
12. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, 1987).
13. S. E. Feller, Y. Zhang, R. W. Pastor, and B. R. Brooks, J. Chem. Phys. 103, 4613 (1995). 10.1063/1.470648
14. Y. Ma, S. Soatto, J. Kosecka, and S. S. Sastry, An Invitation to 3-D Vision (Springer, 2003).
15. B. R. Brooks, J. Comput. Chem. 30, 1545 (2009). 10.1002/jcc.21287
16. See supplementary material at http://dx.doi.org/10.1063/1.4756796 E-JCPSA6-137-034238 for the subroutine implementing SHAPE rigid structure algorithm.
17. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
18. P. Tao, J. F. Fisher, Q. Shi, T. Vreven, S. Mobashery, and H. B. Schlegel, Biochemistry 48, 9839 (2009). 10.1021/bi901118r
19. J. Zhou, S. Reich, and B. R. Brooks, J. Chem. Phys. 112, 7919 (2000). 10.1063/1.481393
20. X. Wu and B. R. Brooks, Biophys. J. 86, 1946 (2004). 10.1016/S0006- 3495(04)74258-7