What is Molecular Dynamics?
Molecular dynamics (MD) simulation numerically solves Newton's equations of motion on an atomistic or similar model of a molecular system to obtain information about its time-dependent properties. MD simulations have provided detailed information on the fluctuations and conformational changes of proteins and nucleic acids. These methods are now routinely used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes. They are also used in the determination of structures from x-ray crystallography and from NMR experiments. Molecular dynamics simulations are very similar to real experiments in many respects.
Today in the literature, one routinely finds molecular dynamics simulations of solvated proteins, protein-DNA complexes as well as lipid systems addressing a variety of issues including the thermodynamics of ligand binding and the folding of small proteins. As well as enzymatic reaction. Molecular dynamics simulation techniques are widely used in experimental procedures such as X-ray crystallography and NMR structure determination. References Alder, B. J. and Wainwright, T. E. J. Chem. Phys. 27, 1208 (1957) Alder, B. J. and Wainwright, T. E. J. Chem. Phys. 31, 459 (1959) Rahman, A. Phys. Rev. A136, 405 (1964) Stillinger, F. H. and Rahman, A. J. Chem. Phys. 60, 1545 (1974) McCammon, J. A., Gelin, B. R., and Karplus, M. Nature 267, 585 (1977)
Applications of molecular dynamics
• Chemical reaction. How molecular combine together. • Electronic properties and dynamics. Car-Parrinello method is used to study electronic properties of materials fully including their dynamics. Biomolecules. Drug design is commonly used in the pharmaceutical industry. Surfaces. Simulation plays a big role in understanding phenomena such as surface reconstructions, surface melting. Fracture. Under mechanical action, solids break into two or more pieces. The fracture process can occur in different ways and with different speeds depending of several parameters. Defects. Defects in crystals--crucial for their mechanical properties and therefore of technological interest--remain a favoured topic.
Fi E ( r1 , r2 , r3 ...)
d Vi dt
mi ai
Vi
dX i dt
• Taking the simple case where the acceleration is constant,
a V dV dt dX dt V V0 a t
t
Introduction to Molecular Dynamics Simulations
分子动力学简介
Get a Feeling about Molecular Dynamics Simulations
Interatomic interactions
MD-Experiments with Argon Gas
• The MD method is deterministic; Once the initial positions and velocities of each atom are known, the state of the system can be predicted at any time in the future.
Classical Mechanics
• Newton’s equation of motion (second law) is given by:
Fi m i a i
• The force can also be expressed as the gradient of the potential energy, and it is more convenient to express as two 1st order equations: ,
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Historical Background
The molecular dynamics method was first introduced by Alder and Wainwright in the late 1950's (Alder and Wainwright, 1957,1959) to study the interactions of hard spheres. Many important insights concerning the behavior of simple liquids emerged from their studies.
The next major advance was in 1964, when Rahman carried out the first simulation using a realistic potential for liquid argon (Rahman, 1964). The first molecular dynamics simulation of a realistic system was done by Rahman and Stillinger in their simulation of liquid water in 1974 (Stillinger and Rahman, 1974).
The first protein simulations appeared in 1977 with the simulation of the bovine pancreatic trypsin inhibitor (BPTI) (McCammon, et al, 1977).
Historical Background (cont’d)
Program MD Call init t=0 !name of program !initialize x, v
X X0
V 0
0
a t d t X 0 V 0 t
1 2
at
2
Numerical Integration Algorithms
• • The potential energy is a function of the atomic positions (3N) of all the atoms in the system. Due to the complicated nature of this function, there is no analytical solution to the equations of motion; they must be solved numerically. A simple molecular dynamics program
Why atomistic MD simulations?
• • MD simulations provide a molecular level picture of structure and dynamics property/structure relationships Experiments often do not provide the molecular level information available from simulations. Simulators and experimentalists can have a synergistic (协同) relationship, leading to new insights into materials properties. Computers are much cheaper than big, expensive laboratories, hence simulation can and does save industry significant expense in the formulation of new and novel materials and pharmaceuticals. Property of Novel materials which have not been synthesized