Purpose: A dynamic collimation system (DCS), which consists of two pairs of orthogonal trimmer blades driven by linear motors has been proposed to decrease the lateral penumbra in pencil beam scanning proton therapy. The DCS reduces lateral penumbra by intercepting the proton pencil beam near the lateral boundary of the target in the beam's eye view. The resultant trimmed pencil beams are asymmetric and laterally shifted, and therefore existing pencil beam dose calculation algorithms are not capable of trimmed beam dose calculations. This work develops a method to model and compute dose from trimmed pencil beams when using the DCS. Methods: MCNPX simulations were used to determine the dose distributions expected from various trimmer configurations using the DCS. Using these data, the lateral distribution for individual beamlets was modeled with a 2D asymmetric Gaussian function. The integral depth dose (IDD) of each configuration was also modeled by combining the IDD of an untrimmed pencil beam with a linear correction factor. The convolution of these two terms, along with the Highland approximation to account for lateral growth of the beam along the depth direction, allows a trimmed pencil beam dose distribution to be analytically generated. The algorithm was validated by computingmore » dose for a single energy layer 5×5 cm{sup 2} treatment field, defined by the trimmers, using both the proposed method and MCNPX beamlets. Results: The Gaussian modeled asymmetric lateral profiles along the principal axes match the MCNPX data very well (R{sup 2}≥0.95 at the depth of the Bragg peak). For the 5×5 cm{sup 2} treatment plan created with both the modeled and MCNPX pencil beams, the passing rate of the 3D gamma test was 98% using a standard threshold of 3%/3 mm. Conclusion: An analytical method capable of accurately computing asymmetric pencil beam dose when using the DCS has been developed.« less