A protocol to simulate the lithiation of amorphous Si at room temperature is presented. One important step in the protocol is the identification of spherical voids in the lithiated structure. The protocol is simple, easily implemented and automated, and can be used with any modeling code capable of structural optimization. The protocol was used in conjunction with density functional theory and projector augmented wave data sets to accurately reproduce the potential composition curve of an experimental Li/LixSi electrochemical cell at room temperature. Volume changes as a function of lithiation obtained from the protocol were also in good agreement with experiment. Based on the agreement with experiment, the protocol appears to yield structures representative of amorphous LixSi obtained when lithiating Si at room temperature.