%%% --- Biophysics of Macromolecules --- %%%
%%% --- LMU - Sommersemester 2020    --- %%%
%%% --- Prof. Lipfert                --- %%%
%%%
%%% Solutions to 
%%% Problem set 1, Problem 3
%%% Lennard-Jones potential

clc;clf;clear;

%%% Define Lennard-Jones parameters

epsilon = 1.66*10^(-21);  %%% in J
sigma   = 3.4*10^(-10);   %%% in m

%%% Convert to appropriate units of the problem; 
%%% For example: Angstroems and kcal/mol
epsilon = epsilon / (6.9477*10^(-21));
sigma   = sigma / 10^(-10);


r = 2:0.01:5;
E = 4*epsilon*((sigma./r).^12 - (sigma./r).^6);


%%% Plot the result
plot(r,E, 'b-', 'linewidth', 2)
axis([2.5 5 -0.5 3 ])
grid on

%%% Note that the default labels sizes in most plotting programs are too
%%% small! Change thge settings to make the plot more readable.
set(gca,'LineWidth', 1,'FontSize', 25, 'FontWeight', 'bold', 'TickLength',[0.02 0.02])
ylabel('Energy (kcal/mol)');
xlabel('Distance (A)');

print(figure(1),'-r300','-dpng', 'Lennard-Jones-Potential.png')