1) The document describes an NVT molecular dynamics simulation of an argon system using the Lennard-Jones potential.
2) Velocities are rescaled after each Verlet step to maintain a fixed temperature using the formula provided.
3) 256 argon atoms were initialized on a 7x7x7 lattice with random velocities at a fixed temperature and the simulation was run for 100,000 time steps with a time step of 1x10-5.
4) Plots show the kinetic, potential, and total energies remain constant over time in the NVT ensemble as expected, while the total energy drifts in the NVE ensemble due to errors from the large time step size.
Original Description:
NVT Simulation of Argon
Using Lennard-Jones Potential
1) The document describes an NVT molecular dynamics simulation of an argon system using the Lennard-Jones potential.
2) Velocities are rescaled after each Verlet step to maintain a fixed temperature using the formula provided.
3) 256 argon atoms were initialized on a 7x7x7 lattice with random velocities at a fixed temperature and the simulation was run for 100,000 time steps with a time step of 1x10-5.
4) Plots show the kinetic, potential, and total energies remain constant over time in the NVT ensemble as expected, while the total energy drifts in the NVE ensemble due to errors from the large time step size.
1) The document describes an NVT molecular dynamics simulation of an argon system using the Lennard-Jones potential.
2) Velocities are rescaled after each Verlet step to maintain a fixed temperature using the formula provided.
3) 256 argon atoms were initialized on a 7x7x7 lattice with random velocities at a fixed temperature and the simulation was run for 100,000 time steps with a time step of 1x10-5.
4) Plots show the kinetic, potential, and total energies remain constant over time in the NVT ensemble as expected, while the total energy drifts in the NVE ensemble due to errors from the large time step size.
Using Lennard-Jones Potential Requirement The system satisfies periodic boundary conditions.
Implement NVT simulation by modifying the program Time Evolution of System
previously written for NVE study of Argon system using Lennard-Jones interaction potential. Verlet integration is used for calculating the trajectories of particles in molecular dynamics NVT Simulation simulations. This algorithm calculates the positions and velocities using iterative method as shown below: A simple method for fixing the kinetic temperature of the system in MD is to rescale the velocities after each r (t + ∆ ) = 2 r (t ) + r (t − ∆ ) + a(t ) ∆2 Verlet step using the formula: r (t + ∆ ) − r (t − ∆ ) − T fixed − v(t ) = [2] V rescaled = ⋅ V current [1] 2∆ Tcurrent here the current temperature is calculated from the It is seen that for calculating r (t + ∆ ) we need r (t ) kinetic energy. This rescaling makes sure that the and r (t − ∆ ) . So we need a different method to get temperature remains fixed at the desired value ( T fixed ) r (t ) using r (t − ∆ ) , for this I chose the Taylor’s after each Verlet step. method for calculating the positions at the first time- step using the formula: Implementation r (t ) = r (t − ∆ ) + ∆ v(t − ∆ ) [3] When an MD simulation is started for the very first time, one needs to specify the initial arrangement of r (t − ∆ ) is calculated using initialization of Argon the atoms in space, as well as their initial velocities. atoms on 7x7x7 lattice. Below I mention the initial conditions that were used in my simulation. Knowledge from Assignment-2 • Atoms were arranged on a 7x7x7 lattice. Only 256 Optimum value of time-step ∆ to be used depends on lattice sites were used to place atoms and rest were the system and the computer resources. It is possible left unoccupied. to get very small errors in the calculations by choosing small ∆ , but the drawback is that it takes a • The initial potential energy is calculated using the larger amount of time to do simulations and to reach Lennard-Jones potential. Kinetic energy is calculated equilibrium. using the temperature T fixed (=2.58). I choose the value of ∆ =1.0 x 10-5 and performed the • Velocity (calculated from K.E) was distributed simulations for a total of 1.0x105 time-steps. among N atoms equally in magnitude. The directions of velocities for N atoms are chosen randomly. 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)
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