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The atmospheric Green's function method is a technique for modeling the response of the atmosphere to changes in the spatial field of surface temperature. While early studies applied this method to changes in atmospheric circulation, it has also become an important tool to understand changes in radiative feedbacks due to evolving patterns of warming, a phenomenon called the "pattern effect." To better study this method, this paper presents a protocol for creating atmospheric Green's functions to serve as the basis for a model intercomparison project, GFMIP. The protocol has been developed using a series of sensitivity tests performed with the HadAM3 atmosphere‐only general circulation model, along with existing and new simulations from other models. Our preliminary results have uncovered nonlinearities in the response of the atmosphere to surface temperature changes, including an asymmetrical response to warming versus cooling patch perturbations, and a change in the dependence of the response on the magnitude and size of the patches. These nonlinearities suggest that the pattern effect may depend on the heterogeneity of warming as well as its location. These experiments have also revealed tradeoffs in experimental design between patch size, perturbation strength, and the length of control and patch simulations. The protocol chosen on the basis of these experiments balances scientific utility with the simulation time and setup required by the Green's function approach. Running these simulations will further our understanding of many aspects of atmospheric response, from the pattern effect and radiative feedbacks to changes in circulation, cloudiness, and precipitation. Plain Language Summary: Many properties of the atmosphere are affected by the temperature of the ocean surface. Knowing how strong these effects are would help us to better predict global warming. The response to a given surface warming depends on where the warming occurs. To account for this, researchers sometimes simulate the response to individual patches of warming and then assume the response to an arbitrary warming pattern can be summed together from these patch responses. This is sometimes called the atmospheric Green's function method, and it works well at recreating the atmospheric response to historical temperature changes. We are organizing a Green's Function Model Intercomparison Project (GFMIP), in which participants will apply the method consistently for many climate models. This paper presents the GFMIP protocol. In the course of developing this protocol, we found that the atmospheric response to warming is not proportional in all cases: the response to surface warming is not the opposite of the response to surface cooling; warming twice as much doesn't cause twice as much of a response; and making a patch of warming twice as large doesn't cause twice as large a response. GFMIP will help us figure out how to account for this nonlinearity. Key Points: The Green's Function Model Intercomparison Project (GFMIP) explores the atmospheric response to surface temperature patch perturbationsThis paper presents the GFMIP protocol, which was generated using insights from past studies and new sensitivity testsGreen's functions reconstruct the response to historical temperatures, but nonlinearities can affect responses to other warming patterns [ABSTRACT FROM AUTHOR]