The PCB file needs to be converted into a compatible format of simulator software. For example, .HYP file format of PCB is needed to simulate in Hyperlynx and SPD file format of PCB is required to simulate in Sigrity. Once the PCB file is loaded in the simulation tool, check the stack-up that matches the PCB stack-up and define the dielectric constant, Dk and dissipation factor, and Df of PCB material. The tool extracts wrong models, if the preceding points are not defined properly. Some tools run the simulations on PCB file itself like Hyperlynx and some tools need S-parameter files of DDR3 traces to continue the simulations. To extract S-parameter models of PCB traces assign the ports on both sides of the traces and extract the S-parameter models of traces.
The following tools can be used to extract S-parameter models of PCB traces:
Sigritys PowerSI