The atmospheric component of Energy Exascale Earth System Model (E3SM) version 1 (EAM1) has included many new features in the physics parameterizations compared to its predecessors. Potential complex nonlinear interactions among the new features create a significant challenge for understanding the model behaviors and parameter tuning. Using the one-at-a-time method, the benefit of tuning one parameter may offset the benefit of tuning another parameter, or the improvement in one target variable may lead to degradation in another target variable. To better understand the EAM1 model behaviors and physics, we conducted a large number of short simulations (3 days) in which 18 parameters carefully selected from parameterizations of deep convection, shallow convection and cloud macrophysics and microphysics were perturbed simultaneously using the Latin Hypercube sampling method. From the Perturbed Parameters Ensemble (PPE) simulations and use of different skill score functions, we identified the most sensitive parameters, quantified how the model responds to changes of the parameters for both global mean and spatial distribution, and estimated the maximum likelihood of model parameter space for a number of important fidelity metrics. Comparison of the parametric sensitivity using simulations of different lengths suggests that PPE using short simulations has some bearing on understanding parametric sensitivity of longer simulations. Results from this analysis provide a more comprehensive picture of the EAM1 behavior. The difficulty in reducing biases in multiple variables simultaneously highlights the need of characterizing model structural uncertainty (so-called embedded errors) to inform future development efforts.