Sairam Tangirala
PHYS 8602, set-3
NVT Simulation of Argon
Using Lennard-Jones Potential
Requirement
Implement NVT simulation by modifying the program
previously written for NVE study of Argon system
using Lennard-Jones interaction potential.
NVT Simulation
A simple method for fixing the kinetic temperature of
the system in MD is to rescale the velocities after each
Verlet step using the formula:
− T fixed −
V rescaled = ⋅ V current [1]
Tcurrent
here the current temperature is calculated from the
kinetic energy. This rescaling makes sure that the
temperature remains fixed at the desired value ( T fixed )
after each Verlet step.
Implementation
When an MD simulation is started for the very first
time, one needs to specify the initial arrangement of
the atoms in space, as well as their initial velocities.
Below I mention the initial conditions that were used
in my simulation.
• Atoms were arranged on a 7x7x7 lattice. Only 256
lattice sites were used to place atoms and rest were
left unoccupied.
• The initial potential energy is calculated using the
Lennard-Jones potential. Kinetic energy is calculated
using the temperature T fixed (=2.58).
• Velocity (calculated from K.E) was distributed
among N atoms equally in magnitude. The directions
of velocities for N atoms are chosen randomly.
The system satisfies periodic boundary conditions.
Time Evolution of System
Verlet integration is used for calculating the
trajectories of particles in molecular dynamics
simulations. This algorithm calculates the positions
and velocities using iterative method as shown below:
r (t + ∆ ) = 2 r (t ) + r (t − ∆ ) + a(t ) ∆2
r (t + ∆ ) − r (t − ∆ )
v(t ) = [2]
2∆
It is seen that for calculating r (t + ∆ ) we need r (t )
and r (t − ∆ ) . So we need a different method to get
r (t ) using r (t − ∆ ) , for this I chose the Taylor’s
method for calculating the positions at the first time-
step using the formula:
r (t ) = r (t − ∆ ) + ∆ v(t − ∆ ) [3]
r (t − ∆ ) is calculated using initialization of Argon
atoms on 7x7x7 lattice.
Knowledge from Assignment-2
Optimum value of time-step ∆ to be used depends on
the system and the computer resources. It is possible
to get very small errors in the calculations by
choosing small ∆ , but the drawback is that it takes a
larger amount of time to do simulations and to reach
equilibrium.
I choose the value of ∆ =1.0 x 10-5 and performed the
simulations for a total of 1.0x105 time-steps.
 Results

Plot (1) below shows the time evolution of kinetic,

potential and total energies. It is seen that the kinetic
energy remains a constant at all the time-steps; this is
due the rescaling of velocities after every Verlet step.
Also the potential energy undergoes fluctuations with
time and shows equilibrated behavior after about
40x103 time-steps.

Averaged values of kinetic, potential and total

energies are calculated in the production run and the
table summarizes these values.

Quantity Average Error

Kinetic Energy 990.72 0.00 Plot(2): Comparison of total energy in NVE and NVT
ensembles
Potential Energy 844.44 0.12
Total Energy 146.28 0.12 Finally the deviations of the total energy can be
understood by having a look the plot (3) which shows
the time-propagation of error in the calculation of total
energy. In particular it can be noted that for ∆ =10-5
the equilibrated total energy has a large errors. This
explains why the equilibrated total energy of NVE
ensemble does not converge towards the constraint
fixed value.

Plot(1): Time evolution of energies

Plot (2) shows the comparison of the total energy

calculated in NVE and NVT ensembles. The
constraint total energy of NVE ensemble is also
shown for comparison.
Plot(3): Time-propagation of error in E*
It is see that in NVE simulation the average total
energy is not closer to fixed value (E*= 101.79) even Statistical error bars in energy calculations are small
after the equilibrium is reached. This deviation is due because I have very large production run (=60.0x104
to Verlet method employing time-step ∆ =1.0x10-5 in time-steps). The systematic errors in energy
the simulation. calculations are observed at large time steps. These
errors are due to Verlet’s method.
Quantity NVE NVT
Total Energy 127.59(0.45) 146.28(0.12)