Download Molecular Dynamics: why and how

Molecular Dynamics: why and how
Computer simulations have been working as the complement to conventional experiments over
the years. Computer simulations are getting more and more popular in academia and industries.
Computational Fluid Dynamics (CFD) is a well known field for research today. Industries now
use this tool to mitigate the research and development costs. Another field, which is emerging in
a rapid manner, is Molecular Dynamics (MD) simulation. Computer simulations are being
carried out in the hope of understanding the properties of assemblies of molecules in terms of
their structure and the microscopic interactions between them. This eventually enables us to
learn something new, something that cannot be found out in other ways. The two main families
of simulation technique are molecular dynamics (MD) and Monte Carlo (MC). To avoid
complexity it can be said in a simpler way that MD gives us some obvious advantages than MC.
This is basically a “Computational Experiment”. We can predict and understand molecular
behavior and compare / interpret experimental observations. By simulating atomic and molecular
motions, we can gain atomistic insight into molecular structure and kinetics. Powerful
experimental techniques (X-ray diffraction, NMR) can resolve atomic structure, but not
dynamics.
Why MD is used?
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Materials property prediction - bulk modulus, surface tension, shear viscosity, thermal
conductivity, flow, gelation
Biomolecular modeling - protein folding, viral capsids, !! cell membranes, ion transport
Ligand and drug design - docking, interaction, sterics
High-throughput molecular screening - drugs, surfactants, self-assembling materials
MD is now a standard tool in pharma, nuclear, chemical, oil, aerospace, electronics, and plastics.
MD is maturing into an “off-the-shelf” tool similar to the emergence of CFD in the 90’s
First MD simulation
Alder & Wainwright (1957) invent molecular dynamics and perform first simulations of the hard sphere
fluid.
Basic Principle:
The basic idea of MD is quite simple as it uses classical mechanics to predict the
thermodynamics properties. Basically you will need three things to run molecular dynamics
simulation.
1. An initial system configuration (The initial position, velocity of the atoms)
2. Interactions potential for system (How the particles react with each other)
3. A way to integrate Newton’s equation of motion (F=ma)
Molecular Dynamics: why and how
Classical MD treats atoms as point particles that move deterministically via Newton’s equations
of motion. Here, the verlet algorithm technique is used to integrate the equation of motion. This
algorithm is quite simple in nature. By integrating, we can predict how the atom will behave after
a certain time step. This integration is performed for a small time step and run for a large number
of steps, which needs strong computation. That’s why this simulation is carried out using a
simple computer (desktop/laptop/windows/mac/linux) or parallel clusters (linux). So we solve
Newton’s equations by numerical integration. So the basic algorithm should be:
Limitations of MD: No electrons and so no chemical reactions, Time and length scale
limitations, Statistical significance of single trajectories
How one should start?
Well, there are various software packages available to carry out the molecular simulation.
GROMACS, AMBER, LAMMPS etc. Most of them are suitable for biological research.
LAMMPS is suitable for metal atoms. The principle problem one might face is that LAMMPS
has no GUI (Graphical User Interface). You will have use the terminal (Linux/mac) or cmd
(windows), which takes some time to be familiar. The best way to start the process is by surfing
through the internet and trying various hands-on examples. Even LAMMPS comes with a built
in example directory. Besides their website is great and the manual has all the documentation
you will need for your code.
Molecular Dynamics: why and how
The simulation happens in two steps. At first you will write your code in any available software.
In case of LAMMPS this code is called the input script. This script is run to obtain different
thermodynamic properties of your system through numerical integration.
In the second step you will want to visualize your result. Hence, you can use another bunch of
visualizing software packages (VMD, OVITO etc.) VMD is very popular among researchers.
The overall process will take time and perseverance. But the task is really enjoyable. More and
more researchers from renowned universities around the world are getting involved with
molecular simulations. So if materials seem interesting to you and you want to play with new
materials, smart materials MD should be your first choice. You can always start from the scratch
and at some point contact any potential supervisor for the research topic. If you know the
ingredients you will know how to cook!!!
For basic reading: Molecular Dynamics Simulation: elementary methods, J M Haile; The art of
molecular dynamics, D. C. Rapaport, LAMMPS Manual.
Reference: Dr. Ferguson’s lecture, Elements of Integrated Computational Materials
Engineering Workshop, UIUC, 2014