5 Basics of Molecular Modeling and Molecular Simulation
199
is also manifested in creating systems to investigate theories using many approximations and ideal conditions, such as the Ising model. The usage of simulated
computational methods allows perceptual understanding for the properties under
these circumstances, leading to better comprehension for the fundamental concepts
in theoretical physics.
To sum up, computational physics is gaining its importance with its unique and
irreplaceable role in connecting theoretical and experimental physics. Its major functions may be concluded into four basic aspects: (1) solving analytical equations
numerically; (2) simulating many-body systems to obtain more realistic results; (3)
simulating under extreme conditions; and (4) simulating systems with many approximations or under ideal conditions. With the development of information technology
that dramatically increases the power of parallel computing, computational physics
will certainly have a rosy prospect in upcoming physics researches. It is thus vital
for future researchers to acknowledge its significance and learn to better understand
as well as make better usage of it in their respective studies.
5.1.2 Molecular Simulations: Studying Physical Properties
at the Molecular Level
As described above, computational physics basically includes two aspects: providing
numerical solutions to analytical equations and conducting computer simulation. To
study fundamental principles of statistical physics and to understand certain physical
properties of materials, computer simulations are of much significance. All materials
simulations are roughly conducted at three temporal and spatial levels: macroscopic,
mesoscopic, and microscopic. It is vital to make such a division for computer simulations in order to determine the correct parameters in use, for the systems at different
levels vary dramatically in terms of their mechanical, thermodynamic, and electromagnetic properties. In this chapter, we will focus mainly on molecular simulations
dealing with materials at the microscopic level with the resolution of atoms, the
mechanisms of different types of molecular simulations, and their applications in
soft-matter physics.
Types of molecular simulations with especial significance in computer simulations
are Monte Carlo (MC) simulations and molecular dynamics (MD) simulations. The
inclusion of such simulations provides researchers with two fundamentally different
measures in dealing with different problems, the differences and usages of which will
also be further demonstrated and introduced in the following parts of this chapter.
A basic knowledge that most researchers should have acquired when investigating
into computer simulation is the vitality of importance sampling for the Boltzmann
distribution, which to a large extent signifies that the basis of molecular simulation
resides in statistical physics. Thus, a good understanding of statistical physics is vital
for researchers to utilize molecular simulations efficiently in their scientific investigations. On the other hand, a good molecular model is prerequisite for molecular
199
is also manifested in creating systems to investigate theories using many approximations and ideal conditions, such as the Ising model. The usage of simulated
computational methods allows perceptual understanding for the properties under
these circumstances, leading to better comprehension for the fundamental concepts
in theoretical physics.
To sum up, computational physics is gaining its importance with its unique and
irreplaceable role in connecting theoretical and experimental physics. Its major functions may be concluded into four basic aspects: (1) solving analytical equations
numerically; (2) simulating many-body systems to obtain more realistic results; (3)
simulating under extreme conditions; and (4) simulating systems with many approximations or under ideal conditions. With the development of information technology
that dramatically increases the power of parallel computing, computational physics
will certainly have a rosy prospect in upcoming physics researches. It is thus vital
for future researchers to acknowledge its significance and learn to better understand
as well as make better usage of it in their respective studies.
5.1.2 Molecular Simulations: Studying Physical Properties
at the Molecular Level
As described above, computational physics basically includes two aspects: providing
numerical solutions to analytical equations and conducting computer simulation. To
study fundamental principles of statistical physics and to understand certain physical
properties of materials, computer simulations are of much significance. All materials
simulations are roughly conducted at three temporal and spatial levels: macroscopic,
mesoscopic, and microscopic. It is vital to make such a division for computer simulations in order to determine the correct parameters in use, for the systems at different
levels vary dramatically in terms of their mechanical, thermodynamic, and electromagnetic properties. In this chapter, we will focus mainly on molecular simulations
dealing with materials at the microscopic level with the resolution of atoms, the
mechanisms of different types of molecular simulations, and their applications in
soft-matter physics.
Types of molecular simulations with especial significance in computer simulations
are Monte Carlo (MC) simulations and molecular dynamics (MD) simulations. The
inclusion of such simulations provides researchers with two fundamentally different
measures in dealing with different problems, the differences and usages of which will
also be further demonstrated and introduced in the following parts of this chapter.
A basic knowledge that most researchers should have acquired when investigating
into computer simulation is the vitality of importance sampling for the Boltzmann
distribution, which to a large extent signifies that the basis of molecular simulation
resides in statistical physics. Thus, a good understanding of statistical physics is vital
for researchers to utilize molecular simulations efficiently in their scientific investigations. On the other hand, a good molecular model is prerequisite for molecular