Hello,
I am a master’s student new to MD simulations, and I have a few questions about building a multicomponent membrane system.
Background:
I have an existing POPC bilayer (100 lipids/leaflet) built with CHARMM-GUI, using CHARMM36m force field, TIP3P water, 310K NPT ensemble in GROMACS 2021.4.
Question 1 -Building method:
I need to add a small molecule co-solvent to the water phase of my existing bilayer system. What is the recommended approach:
- CHARMM-GUI Multicomponent Assembler
- gmx insert-molecules with -replace SOL
- Another method entirely?
Are there any tutorials or published papers that describe this workflow clearly?
Question 2- Small-molecule interaction-
I want to add a small-molecule drug into the bilayer to see the interaction of the drug with the lipids. How can I add other components into the bilayer other than lipids?
Question 3 -Many components:
With 5+ molecular components of varying concentrations, is there a recommended order or strategy for building the system to avoid clashes and ensure proper equilibration? I planned to take my base system (membrane only) and simulate every component I add. Does that sound applicable?
Thank you in advance for any guidance.