PurposeWe developed a 4‐dimensional dynamic dose (4DDD) calculation model for proton pencil beam scanning (PBS). This model incorporates the spill start time for all energies and uses the remaining irradiated spot time model instead of irradiated spot time logs. This study aimed to validate the calculation accuracy of a log file‐based 4DDD model by comparing it with dose measurements performed under free‐breathing conditions, thereby serving as an alternative approach to the conventional log file‐based system.MethodsThree cubic verification plans were created using a heterogeneous block phantom; these plans were created using 10 phase 4D‐CT datasets of the phantom. The CIRS dynamic platform was used to simulate motion with amplitudes of 2.5, 3.75, and 5.0 mm. These plans consisted of eight‐ and two‐layered rescanning techniques. The lateral profiles were measured using a 2D ionization chamber array (2D‐array) and EBT3 Gafchromic films at four starting phases, including three sinusoidal curves (periods of 3, 4, and 6 s) and a representative patient curve during actual treatment. 4DDDs were calculated using in‐house scripting that assigned a time stamp to each spot and performed dose accumulation using deformable image registration. Furthermore, to evaluate the impact of parameter selection on our 4DDD model calculations, simulations were performed assuming a ±10% change in irradiation time stamp (0.8 ± 0.08 s) and spot scan speed. We evaluated the 2D gamma index and the absolute point doses between the calculated values and the measurements.ResultsThe 2D‐array measurements revealed that the gamma scores for the static plans (no motion) and 4DDD plans exceeded 97.5% and 93.9% at 3%/3 mm, respectively. The average gamma score of the 4DDD plans was at least 96.1%. When using EBT3 films, the gamma scores of the 4DDD model exceeded 92.4% and 98.7% at 2%/2 mm and 3%/3 mm, respectively. Regarding the 4DDD point dose differences, more than 95% of the dose regions exhibited discrepancies within ±5.0% for 97.7% of the total points across all plans. The spot time assignment accuracy of our 4DDD model was acceptable even with ±10% sensitivity. However, the accuracy of the scan speed, when varied within ±10% sensitivity, was not acceptable (minimum gamma scores of 82.6% and maximum dose difference of 12.9%).ConclusionsOur 4DDD calculations under free‐breathing conditions using amplitudes of less than 5.0 mm were in good agreement with the measurements regardless of the starting phases, breathing curve patterns (between 3 and 6 s periods), and varying numbers of layered rescanning. The proposed system allows us to evaluate actual irradiated doses in various breathing periods, amplitudes, and starting phases, even on PBS machines without the ability to record spot logs.