To begin, use a web browser to visit the charmm-gui. org website. Create and activate your free account before building your first set of files.
Go to the top menu, navigate to the input generator and select membrane builder from the available options on the left side of the screen. Select the bilayer builder to construct a lipid bilayer, then select the membrane only system and store the generated job ID for future access. Visualize the systems during every step of the building process by clicking view structure located at the top of the page.
Consistently inspect for missing components or errors in patch size. Select the heterogeneous lipid option regardless of whether to build a single component bilayer, then choose a rectangular box type. For hydration, select 45 water molecules per lipid, which is ample for a fully hydrated bilayer.
Now set the length of XY based on the number of lipid components. Determine the number of lipids needed for each lipid species based on the pre-planned model. To represent the endoplasmic reticulum and eukaryotic cells, a combination of 336 DOPC, 132 DPPE, 60 cholesterol, and 72 POPI lipids was used in the PI model while 330 DOPC, 126 DPPE, 54 cholesterol, 66 POPI, and 24 DOPS lipids were used for the PIPS model.
Input the desired number of molecules for the upper and lower leaflets in the two boxes next to the lipid name to create a symmetric membrane composition. Then navigate to the top of the lipid species list and initiate the action by clicking on the show the system info button. Using CHARMM-GUI, validate the total count of lipids in each leaflet in the symmetric bilayer.
Continue clicking the next screens to set the desired values for temperature and pressure for simulation and the syntax for the simulation files according to the molecular dynamics engine of choice. For instance, GROMACS. Download the resulting files and transfer them to the computer cluster.
Use selected software, for instance, visual molecular dynamics or PyMOL to visualize the final system.
