This paper introduces Membrane Builder, a web-based tool for automatically building and simulating protein/membrane complexes for molecular dynamics (MD) simulations. Membrane Builder is part of the CHARMM-GUI website (http://www.charmm-gui.org) and provides a graphical user interface (GUI) for users to create realistic membrane systems with various types of membrane proteins. The tool allows users to define system size, shape, ion concentration, and lipid type, and automatically generates lipid bilayers, pore water, bulk water, and ions. The process is generalized and automated, enabling the creation of realistic membrane systems in 5 minutes to 2 hours, depending on the system size. The tool is designed to be user-friendly, with default values that provide reasonable options for both non-expert and expert users. The efficacy of Membrane Builder is demonstrated by its application to 12 transmembrane and 3 interfacial membrane proteins, with fully equilibrated systems available on the CHARMM-GUI website. The tool uses two methods for building lipid bilayers: the insertion method, which creates a hole in a pre-equilibrated lipid bilayer and inserts the protein into the hole, and the replacement method, which distributes lipid-like pseudo atoms around the protein and replaces them with lipid molecules. The replacement method is more flexible and can be used for a wide range of membrane proteins, including transmembrane and interfacial proteins. The insertion method is faster and generates a pre-equilibrated lipid bilayer, but is limited to proteins with a regular and cylindrical shape. The tool also includes a pore water generation method that allows for the accurate simulation of water molecules in the transmembrane region of membrane proteins. The tool has been tested with a variety of membrane proteins, and the results show that it is effective in generating realistic membrane systems for MD simulations. The tool is freely available and can be used by researchers to study the structure and function of membrane proteins in their native environments.This paper introduces Membrane Builder, a web-based tool for automatically building and simulating protein/membrane complexes for molecular dynamics (MD) simulations. Membrane Builder is part of the CHARMM-GUI website (http://www.charmm-gui.org) and provides a graphical user interface (GUI) for users to create realistic membrane systems with various types of membrane proteins. The tool allows users to define system size, shape, ion concentration, and lipid type, and automatically generates lipid bilayers, pore water, bulk water, and ions. The process is generalized and automated, enabling the creation of realistic membrane systems in 5 minutes to 2 hours, depending on the system size. The tool is designed to be user-friendly, with default values that provide reasonable options for both non-expert and expert users. The efficacy of Membrane Builder is demonstrated by its application to 12 transmembrane and 3 interfacial membrane proteins, with fully equilibrated systems available on the CHARMM-GUI website. The tool uses two methods for building lipid bilayers: the insertion method, which creates a hole in a pre-equilibrated lipid bilayer and inserts the protein into the hole, and the replacement method, which distributes lipid-like pseudo atoms around the protein and replaces them with lipid molecules. The replacement method is more flexible and can be used for a wide range of membrane proteins, including transmembrane and interfacial proteins. The insertion method is faster and generates a pre-equilibrated lipid bilayer, but is limited to proteins with a regular and cylindrical shape. The tool also includes a pore water generation method that allows for the accurate simulation of water molecules in the transmembrane region of membrane proteins. The tool has been tested with a variety of membrane proteins, and the results show that it is effective in generating realistic membrane systems for MD simulations. The tool is freely available and can be used by researchers to study the structure and function of membrane proteins in their native environments.