泛素是一種小型的調節型蛋白質，它在所有的生物組織中都可以發
現到它的存在。因此我們從蛋白質銀行 (protein data bank)找出泛
素的真實數據，然後利用視覺分子模擬軟體(Visual Molecular
Dynamics) 看見其分子結構，還可以看到它溶於水中的情形。最後，
我們可以利用 Steered Molecular Dynamics 去了解泛素在生物體中
有可能的結構變化。

Ubiquitin is a small regulatory protein that has been found in almost all tissues
(ubiquitously) of eukaryotic organisms [19]. The real data of ubquitin is obtained
from the protein data bank (PDB). Then, the protein is simulated by the software
Visual Molecular Dynamics (VMD). We can see the molecular structure and the
protein solvated in water. We can study the dynamical properties of the protein by
using the software Steered Molecular Dynamics.

Contents
1 Introduction ........................................... 4
2 Ubiquitin ........................................... 5
3 Visual Molecular Dynamics .............................. 6
4 NAMD .................................................. 12
5 What is Needed ........................................ 15
6 Steered molecular dynamics ............................ 20
7 Result ................................................ 23
Appendix ................................................ 25
8 References .................... ....................... 69

[1] A. Aksimentiev et al, Using VMD[Online],Available:http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf, 2011.
[2] M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids. Oxford University Press,1987.
[3] C. Bartels, Analyzing biased Monte Carlo and molecular dynamics simulations, 2000.
[4] F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, J. E. F. Meyer, M. D. Brice, J. R. Rodgers,O. Kennard, T. Shimanouchi, and M. Tasumi, The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535–542, 1977.
[5] M. Bhandarkar et al, NAMD User’s Guide (Version 2.9) [Online]. Available:http://www.ks.uiuc.edu/Research/namd/2.9/ug.pdf, 2012.
[6] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M.Karplus. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2):187–217, 1983.
[7] A. T. Brunger, X-PLOR, Version 3.1, A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1992.
[8] W. Humphrey, A. Dalke, and K. Schulten, VMD - Visual Molecular Dynamics, J. Molec. Graphics, 1996.
[9] S. Kumar et al, THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method". Journal of Computational Chemistry 13 (8): 1011–1021, 1992.
[10] J. Leszczynski. Computational chemistry: reviews of current trends, Volume 9, 54–56, 2005.
[11] G. Nienhaus, Protein-ligand interactions: methods and applications, 54–56, 2005.
[12] J. Phillips et al, NAMD TUTORIAL Windows Version [Online]. Available:http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf , 2012.
[13] T. Schlick, Pursuing Laplace's Vision on Modern Computers, In J. P. Mesirov, K. Schulten and D. W. Sumners. Mathematical Applications to Biomolecular Structure and Dynamics, 218–247, 1966.
[14] T. Schlick, Pursuing Laplace's Vision on Modern Computers, In J. P. Mesirov,K. Schulten and D. W. Sumners. Mathematical Applications to Biomolecular Structure and Dynamics, IMA Volumes in Mathematics, 218–247, 1996.
[15] NAMD, http://www.ks.uiuc.edu/Research/namd/.
[16] The Nobel Prize in Chemistry 2004, Nobelprize.org. Retrieved 2010.
[17] The Nobel Prize in Chemistry 2004, Popular nformation, Nobelprize.org. Retrieved 2010.
[18] VMD, http://www.ks.uiuc.edu/Research d/allversions/what_is_vmd.html.
[19] Wikipedia, https://en.wikipedia.org/wiki/Ubiquitin.
[20] Wikipedia, http://en.wikipedia.org/wiki/Molecular_dynamics.