close all;
style{1} = 'bo-';
style{2} = 'go-';

for i=1:3
    % don't do number 1, it explodes!
    if ne(1,i)
        dlmwrite('subtracted_traj_sum30.txt',cytoD{i}.trajectory,'\t');
        newGetMSD;
        [temp{1}.TauVector, tempOmegaVector, MSD{1}.temp, ...
            Alpha{1}.temp, GpMason{1}.temp, GppMason{1}.temp] = newGetGstar2;
        
    end
        dlmwrite('subtracted_traj_sum30.txt',untreated{i}.trajectory,'\t');
        newGetMSD;
        [TauVector{2}.temp, OmegaVector{2}.temp, MSD{2}.temp, ...
            Alpha{2}.temp, GpMason{2}.temp, GppMason{2}.temp] = newGetGstar2;
end

for i=1:2
figure(1)

if(1) 
   figure(1)
   hold on;
   loglog(TauVector{i}, MSD{i}*1e18,style{i});
   xlabel('\tau'); ylabel('MSD [nm^2]'); title('MSD');
end

figure(2)
hold on;
loglog(OmegaVector{i}, GpMason{i}, style{i})
title(' Storage Modulus G prime ');
xlabel('\omega'); ylabel('pascals');

figure(3)
hold on;
loglog(OmegaVector{i}, GppMason{i}, style{i})
title(' Loss Modulus G double prime ');
xlabel('\omega'); ylabel('pascals');

figure(4)
hold on;
semilogx( OmegaVector{i}(1,:), Alpha{i}(1,:),style{i} )
xlabel('\omega'); ylabel('\alpha'); title('\alpha vs \omega');
end

for j=1:4
    figure(j)
    legend('untreated','cytoD','Location','Best')
end

