The program MDS_init.f90 generates the initial positions for a 3D cube of atoms, and MDS_EOM.f90 computes the Equations Of Motion of said cube via Verlet algorithm, taking Lennard-Jones interactions into account.

Download the last version from:
https://github.com/pablogila/Molecular_Dynamics_Sim

Compile the program and execute as follows:

First, we assign the initial positions, creataing the initial files for the cube
gfortran tipos.f90 MDS_init.f90
./a.out

Next we execute the Equations Of Motion
gfortran tipos.f90 MDS_EOM.f90
./a.out

Visualize initial cube
xmakemol -f fort.3

Plot histogram of velocities
gnuplot
> plot 'fort.7' u 1:2 w l

Plot histogram of positions
gnuplot
> plot 'fort.8' u 1:2 w l

Plot the kinetic, potential and total energies
gnuplot
> plot "fort.10" u 2:3 w l, "fort.10" u 2:4 w l, "fort.10" u 2:5 w l

Visualize the simulation
xmakemol -f fort.11

fort.3 - initial positions in xyz, for xmakemol
fort.4 - initial positions
fort.7 - histogram of velocities
fort.8 - histogram of positions
fort.9 - initial velocities
fort.10 - energies at each time step
fort.11 - positions at each time step