Paper title: Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
Journal: Angew. Chem. Int. Ed. Engl., Vol. 29, No. 9. (1990), pp. 992-1023

Author(s): Wilfred F. van Gunsteren[1,2] and Herman J. C. Berendsen[1]
[1] Department of Physical Chemistry, University of Groningen, Nijenborgh 16, NL-9747 AG Groningen (The Netherlands)
[2] Department of Physics and Astronomy, Free University, De Boelelaan 1081, NL-1081 HV Amsterdam (The Netherlands)

Summary:
The paper consists of detailed explanation of the steps and considerations for performing computer simulations in general. But majority of this talk about molecular dynamics simulation (MDS).

Computer simulation of the dynamics of a molecular system is covered by computational chemistry and physics. Here, a mathematical model of the real world is formulated then evaluated using numerical methods. A crucial part of creating models is how it was formulated ? the assumptions, simplifications and approximations used. So in this paper, these points are discussed in detail.

The authors introduce computer simulation of molecular systems by presenting its history, purpose and reliability. In addition, they tackle the two basic problems in computer simulations of fluid-like molecular systems: size of configuration space and accuracy of molecular model. Then the paper enumerates the assumptions, approximations and limitations of the simulation. These include system properties such as thermodynamic quantities as well as atomic properties such as position and mobility of crystals, distance in solution, orientation of molecular fragments and diffusion.

For molecular dynamics, trajectories of atoms are calculated using force fields. Both bonded and long-range interactions are considered but their treatments differ from each other. Afterwards, three types of boundary conditions (vacuum, periodic and extended wall region) and two types of MD (constant-temperature and constant-pressure) were described. Integration schemes for both molecular and stochastic dynamics, application of constraints as well as multiple time step algorithms were also explained.

The paper also gives examples on how to apply MDS and other computer simulations in Chemistry and Physics and how to interpret its results. It also considers the future developments that may be done to computer simulation of molecular systems such as doing quantum simulations, improving system size and time-scale of simulations, enhancing accuracy of molecular models and force fields, employing non-equilibrium approach and increasing the computing power.
    

Contribution and application:

MDS is useful for looking into the SWRO process on a molecular level. Fouling layer development as well as particle movement may be comprehensively observed using MDS.



By: Hannah Ebro
hannah@gist.ac.kr