You have now hopefully been successful in building and simulating a simple membrane protein system. Note that 1 ns of simulation is exceptionally short for any system, especially a membrane protein. Lipid equilibration can take upwards of 50-100 ns. The timeframe used here is for instructional purposes only, and the data you generate likely have no physical meaning, since the timeframe is too short. The .mdp files provided here serve as examples only, and should not be considered broadly applicable to all systems. Review the literature and the GROMACS manual for adjustments to these files for efficiency and accuracy purposes.

Please be advised that the GROMOS96 53A6 force field as been recently shown to understabilize α-helices. That is, if you were to simulate the system in this tutorial for long enough, the peptide will unfold. This is spurious behavior and has been corrected in the more recent 54A7 parameter set. I wrote this tutorial a long time ago, before the deficiencies with 53A6 were known, but I still believe it serves as a useful example. Combination of Berger lipid parameters with GROMOS96 parameter sets remains a valid approach, provided that one understands the possible problems with the protein force fields.

If you have suggestions for improving this tutorial, if you notice a mistake, or if anything else is unclear, please feel free to email me. Please note: this is not an invitation to email me for GROMACS problems. I do not advertise myself as a private tutor or personal help service. That's what the GROMACS User Forum is for. I may help you there, but only in the context of providing service to the community as a whole, not just the end user.

Happy simulating!