GROMACS version: 2020.5
GROMACS modification: No
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I am currently trying to run a md simulation of a protein binding to a membrane and I can’t find where to start. I currently have these input files
(and other CHARMM-Gui outputs for membrane only development)
Protein.pdb
Membrane.pdb
MembraneIndex.ndx
Membrane.gro
MembraneTopol.top
Lipid1.itp
Lipid2.itp
What do i need to do to simulate this interaction? am i on the right track? Thank you!
I never do protein binding to a membrane, because I simulate mostly only membrane system (without proteins, but I think you should check the tutorials GROMACS Tutorials
You should try to do Tutorial 2: KALP15 in DPPC because this is a system with membrane and protein. First you should build the system, then (I see that you build your system in charmm-gui) then minimize energy, equilibrate and run md simulation like in the tutorial and then analyze some parameters.