Molecular Dynamics Simulation

Lecture 1: Introduction and Potential Model

Dr. T. K. Kundu

MD: Different Type of Simulation

Many Physically-Based Simulations model easily observable real world phenomena. Molecular Dynamics Simulations model things too small for us to observe directly.

MD: Intro
The aim of MD is to calculate how a system of particles (molecules) evolves in time under certain thermodynamic conditions. The starting point is the collection of particles (ensemble) defined through the position of each one of them as well as their velocities. From there we calculate the next position of each particle over a short time interval by solving Newtons equations (strictly classic mechanics)

Why Not Quantum Mechanics?

Modeling the motion of a complex molecule by solving the wave functions of the various subatomic particles would be accurate

2 + U ( x , y , z ) ( x , y , z ) = E ( x , y , z ) 2 m
But it would also be very hard to program and take more computing power than anyone has!

Classical Mechanics
Instead of using Quantum mechanics, we can use classical Newtonian mechanics to model our system. This is a simplification of what is actually going on, and is therefore less accurate. To alleviate this problem, we use numbers derived from QM for the constants in our classical equations.

Molecular Modeling
For each atom in every molecule, we need: Position (r) Momentum (m*v) Charge (q) Bond information (which atoms, bond angles, etc.) Interaction Potential

From Potential to Movement

To run the simulation, we need the force on each particle.
Fi = mi ai

Fi = mi ai
Fi = iV
d ri dV = mi 2 dri dt
2

We use the gradient of the potential energy function (V) to calculate force. Now we can find the acceleration.

Procedure of MD

Basic MD Algorithm
Set initial conditions ri (t2) and v i (t2) Get new forces Fi (ri ) Solve the equations of motion numerically over a short step t ri (t ) ri (t + t ) v i (t ) v i (t + t )
t = t + t

Is t > t max ? Calculate results and finish

Interaction Model: Potentials

ab initio potential
Quantum calculation, DFT etc.

Empirical potential
Comes from quantum calculation/experiments Consistent with continuum Fit the database: elastic moduli, surface energy, etc.

Connection with continuum

Constitutive relation

What is the Empirical Potential/Forcefield?

A single atom will be affected by the potential energy functions of every atom in the system:
Bonded Neighbors Non-Bonded Atoms (either other atoms in the same molecule, or atoms from different molecules)

V ( R ) = Ebonded + E non bonded

Bonded Atoms
There are three types of interaction between bonded atoms: Stretching along the bond Bending between bonds Rotating around bonds

E bonded = E bond stretch + E angle bend + E rotate along bond

Bond Length Potentials

Ebond stretch =
2 pairs ,2

(b b2)

Both the spring constant and the ideal bond length are dependent on the atoms involved.

Bond Angle Potentials

Ebond bend =
angles

K (

The spring constant and the ideal angle are also dependent on the chemical type of the atoms.

Torsional Potentials
E rotate along bond =
2 pairs ,2

K (2 cos( n ))

Described by a dihedral angle and coefficient of symmetry (n=1,2,3), around the middle bond.

Non-Bonded Atoms
There are two potential functions we need to be concerned about between non-bonded atoms: van der Waals Potential Electrostatic Potential

E non bonded = E van der Waals + E electrostatic

The van der Waals Potential

Atoms with no net electrostatic charge will still tend to attract each other at short distances, as long as they dont get too close. Once the atoms are close enough to have overlapping electron clouds, they will repel each other with astounding force One of the most widely used functions for the van der Waals potential is the Lennard-Jones.

The van der Waals Potential

E Lennard Jones Aik C ik = 2 2 r 2 r nonbonded ik ik pairs

The Constants A and C depend on the atom types, and are derived from experimental data.

The Electrostatic Potential

Opposite Charges Attract Like Charges Repel The force of the attraction is inversely proportional to the square of the distance
Coulombs Law

Eelectrostatic

q2 2 q F= 2 2 2 r

qi qk = nonbonded Drik
pairs