Solving a Second Order Differential with Matrix input

I am trying to solve a second order differential using ODE45 in Matlab with matrix as inputs. I am struck with couple of errors that includes :

"In an assignment  A(I) = B, the number of elements in B and
 I must be the same."

Double order differential equations given below:

dy(1)= diag(ones(1,100) - 0.5*y(2))*Co;
dy(2)= -1 * Laplacian(y(1)) * y(2);

Main function call is:

[T,Y] = ode45(@rigid,[0.000 100.000],[Co Xo]);

Here, Co is Matrix of size 100x100 and Xo is a column matrix of size 100x1. Laplacian is a pre-defined function to compute matrix laplacian.

I will appreciate any help in this. Should I reshape input matrices and vectors to fall in same dimensions or something?

~Tushar