Staring from MATLAB R2024b, one of the ways you can specify the initial conditions for simulating a state-space model in the lsim function by a vector xinit having one entry for each state in sys as shown below:
% Initial condition
xinit = 0; % Initial state, x(0) = 0
% Simulate the system response
[y, tOut, x] = lsim(sys1, u, t, xinit);
Refer to the following documentation links to read an example illustrating the same and the details about the initial condition input argument:
