We present a novel formulation, called the WaMPDE, for solving systems with forced autonomous components. An important feature of the WaMPDE is its ability to capture frequency modulation (FM) in a natural and compact manner. This is made possible by a key new concept: that of warped time, related to normal time through separate time scales. Using warped time, we obtain a completely general formulation that captures complex dynamics in autonomous nonlinear systems of arbitrary size or complexity. We present computationally efficient numerical methods for solving large practical problems using the WaMPDE. Our approach explicitly calculates a time-varying local frequency that matches intuitive expectations. Applications to voltage-controlled oscillators demonstrate speedups of two orders of magnitude.