GROMACS version: 2023
GROMACS modification: No
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I conducted a simulation of an ion channel using GROMACS. By default, does the software put water into the channel? If so, what methods can assess the water concentration or flux within the ion channel? I would greatly appreciate any guidance you could provide on this matter.
If you build your system using Charmm-GUI, it has an option to fill the channel with water. However, the channel will usually be filled with water during the minimization and equilibration steps, even without placing water molecules inside the pore. Read more here: Introduction to Membrane-Protein Simulation — GROMACS tutorials https://tutorials.gromacs.org documentation
Thank you very much. I built the system utilizing the Amber99SB force field and simulated the ion channel within an aqueous environment, without a membrane. Is it scientifically inaccurate to conduct simulations of an ion channel without including a membrane?
It is inaccurate because it is not soluble but is a membrane protein, confined within the membrane and has numerous interactions with the surrounding lipids. Additionally, the simulation protocol is also different.