Computational Electrophysiology Setup with GROMACS (.mdp file)

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Dear all and GROMACS Development Team,

I am currently engaged in research involving membrane proteins and am in the process of setting up computational electrophysiology simulations using GROMACS. I have encountered a discrepancy, and I hope you can help clarify.

According to the GROMACS manual, the .mdp file should include three types of ions: K+, Na+, and Cl-. However, in the experimental section of the publication I am following, no potassium ions (K+) are added to the system. Could you please explain the rationale behind including K+ ions in the .mdp file settings despite their absence in the experimental protocol described in the publication?

  1. Publication by GROMACS development team: Redirecting
  2. Reference manual on the official GROMACS web page: Computational Electrophysiology — GROMACS 2019 documentation
  3. the .mdp file in the official GROMACS webpage;
    solvent-group = SOL ; Group containing the solvent molecules
    iontypes = 3 ; Number of different ion types to control
    iontype0-name = NA ; Group name of the ion type
    iontype0-in-A = 51 ; Reference count of ions of type 0 in A
    iontype0-in-B = 35 ; Reference count of ions of type 0 in B
    iontype1-name = K
    iontype1-in-A = 10
    iontype1-in-B = 38
    iontype2-name = CL
    iontype2-in-A = -1
    iontype2-in-B = -1

Thank you for your assistance.

Best regards,
Surapoj

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Dear Surapoj,

The computational electrophysiology setup from the GROMACS manual is only an example and is intended to show that you can define any number of ion types if you wish. Depending on what you want to simulate, you may need two ion types (e.g. Na+ and Cl-, or K+ and Cl-) or even more. For the setup from the publication, you can simply omit the third ion type:

 solvent-group = SOL
 iontypes = 2
 iontype0-name = NA
 iontype0-in-A = -1 ; for example! or put your desired numbers here
 iontype0-in-B = -1
 iontype1-name = CL
 iontype1-in-A = -1
 iontype1-in-B = -1

Best of luck with your simulations!
Carsten

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