[gmx-users] generation of ions additional to solvent molecules

Raag Saluja saluja.raag at gmail.com
Fri Jan 6 07:05:54 CET 2017


I wanted to study the impact of certain ions on a particular protein.
Earlier, I used to simply replace the solvent molecules with the ions.
However, in the current case I need to add a very large number of ions,
which exceeds the number of solvent molecules.So its giving me an error.

The command I used was:

genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np

Is there a way to add ions additional to the solvent molecules, instead of
replacing them?

Thank you and regards,

Raag Saluja

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