normal Martini 3 not that stable with aromatic amino acids?

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1 year 1 month ago #9627 by congwang
Recently I conducted some slab simulations for protein condensates using Maritni model. My condensates are made up of hundreds of very short peptides like WWWW. My simulations always crashed in the production step because of too many LINCS warnings.

Initially, I thought maybe it was because there were so many chains and I didn't relax the system well. But then I decreased the size of the system and only simulated one peptide chain. It also crashed.

One significant pattern of my peptides is they have lots of aromatic rings. I did simulations using the same parameters for other peptides with fewer aromatic rings (like AAAA), they all ran well, not matter condensates simulation or single chain simulation.

So does anyone have ideas if aromatic rings are the reason why my simulations crashed? I'd appreciate any comments or suggestions

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1 year 1 month ago #9630 by congwang
Another interesing thing is, after I added "nstvout = 50000" to the .mdp of the production simulation, there was no lincs warning any more.

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1 year 1 week ago #9648 by pcmartini
I had similar LINCs errors when I tried to make a bilayer with the Martini 3 cholesterol model, and when I changed nstvout from 0 to 50000, the LINCs warnings disappeared and the run was successful. Did you ever find out why this worked? Thank you!

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