Molecular Dynamics Simulation (a brief introduction) by Giff Ransom A Digital Laboratory
by Giff Ransom
“In the real world, this could eventually mean that most chemical experiments are conducted inside the silicon of chips instead of the glassware of laboratories. Turn off that Bunsen burner; it will not be wanted in ten years.”
- The Economist, reporting on the work of the 1998 Chemistry Nobel Prize Awardees
For each atom in every molecule, we need:
To run the simulation, we need the force on each particle.
We use the gradient of the potential energy function.
Now we can find the acceleration.
A single atom will be affected by the potential energy functions of every atom in the system:
There are two potential functions we need to be concerned about between non-bonded atoms:
One of the most widely used functions for the van der Waals potential is the Lennard-Jones. It is a compromise between accuracy and computability.
The Constants A and C depend on the atom types, and are derived from experimental data.
Combine the LJ and
There are three types of interaction between bonded atoms:
Both the spring constant and the ideal bond length are dependent on the atoms involved.
The spring constant and the ideal angle are also dependent on the chemical type of the atoms.
Described by a dihedral angle and coefficient of symmetry (n=1,2,3), around the middle bond.
Using NAMD (Not Another Molecular Dynamics Simulation) and VMD (Visual Molecular Dynamics) from the University of Illinois at Urbana Champaign