normal neutralization of martini protein cg

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1 year 1 month ago - 1 year 1 month ago #7601 by cm
i am following this tutorial
cgmartini.nl/index.php/tutorials-general-introduction/proteins
after solvation i just want to add the only chloride ions.i am not getting the genion commands.how can i do this.
i am just beginner of this force field.can anyone please tell me what will be the commands for neutralisation of martini protein coarse grained system.

can i simply add the martini_v2.0_ions.itp in the system topology file deleting the same no of waters molecules.
thanking you
Last edit: 1 year 1 month ago by cm.

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1 year 1 month ago #7603 by peterkroon
Replied by peterkroon on topic neutralization of martini protein cg
Hi CM,

Have you read the genion help? (gmx genion -h)
Otherwise you can add the number of ions you want directly to your .top (and remove them from W).
You will also need to #include the martini ions itp so gromacs knows which parameters are associated with the ions.

Peter

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