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normal Martini 3 Ions clumping together

  • AlexBW
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1 year 10 months ago #9421 by AlexBW
Martini 3 Ions clumping together was created by AlexBW
So I am attempting to make a membrane in insane with no charged beads as part of the lipids, which I am planning on inserting a protein into once the membranes stability has been confirmed. However I noticed that the ions in the system, NA and CL, have been clumping together to basically form mini salt crystals in the water around the membrane over the course of the simulation, I have run other martini 3 simulations but I have not seen this issue before and am unaware on what is causing it and how to prevent it. The Ions are not interacting with the membrane and I am using the default martini_v3.0.0_ions_v1.itp and martini_v3.0.0_solvents_v1.itp forcefeilds. I am also using equal amounts of NA and CL beads currently in the simulation but am planing on adjusting the ratio to neutralize the system when the protein is inserted in future simulations.
Bead Amounts
W 30090
NA 331
CL 331

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1 year 9 months ago #9429 by paulocts
Replied by paulocts on topic Martini 3 Ions clumping together
Dear AlexBW

Usually this kind of issue is related to wrong settings/parameters in the mdp file, like wrong cutoff or dielectric constant. For instance, a common issue is to comment the epsilon_r = 15 in your mdp file. In this situation, GROMACs will use the default value which is not suitable for Martini. Please use this mdp file here as reference for your simulation:

cgmartini.nl/images/parameters/exampleMD...tini_v2.x_new-rf.mdp

Please use 20 fs as time step and adapts the parameters that can be changed depending on your systems, as thermostat and barostat settings.

Could you please share here the mdp you are using? In this way, we can better debug what is the issue here.

Best regards,

Paulo

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1 year 9 months ago #9444 by AlexBW
Replied by AlexBW on topic Martini 3 Ions clumping together
Paulo, Thanks for the info I went and checked the .mdp file I was using and found that I was using the epsilon_r value that was meant for the martini 2 polarize-able water I seem to have missed changing that when I ran the martini 3 sims.

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