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10 years 9 months ago - 10 years 9 months ago #1761 by satnamphysics
Related to adding ions was created by satnamphysics
I have to add ions in the solution to neutralize it. I want to know that how to add ions in the solution. Actually for non-martini we often use genion to add ions . But for martini there is any special method? I have downloaded gro file of Na+ ion . Kindly tell me how to proceed.

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10 years 9 months ago #1762 by djurre
Replied by djurre on topic Related to adding ions
Using genion should also work for Martini. You won't need any gro file for the ions, they will be added to you existing gro/pdb file. You do need the itp file though.

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10 years 9 months ago #1763 by Clement
Replied by Clement on topic Related to adding ions
Djurre's totally right, genion will works for Martini systems (any system actually) if you precise the amount of ions you want with the -np or -nn flags.

But... If one needs to add ions to a system, here's another solution (to follow exactly what is done by genion):
    Use
grompp one first time on the system (without ion); it will give the total charge of the system.[/ul]
    Modify the system topology by adding an extra line with the corresponding number of counter ions [after the water beads line], and subtracting this number from the total number of water beads.
    Rerun
grompp with the modified topology (it will complain about non-matching names, just add a -maxwarn flag).[/ul]The system is now neutral, and the number of particles didn't change.

Remember that one coarse-grain water bead = four water molecules, and one coarse-grain ion bead = one ion solvated by four water molecules. Topology-wise, it's exactly the same...

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