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

Erik Marklund erik.marklund at kemi.uu.se
Fri Jan 6 11:30:55 CET 2017

Dear Raag,

Where would those extra ions go? If you need a higher number density of ions than the solvent (assuming the box is full of water, plus the protein) you will most likely raise the pressure of the system to bizarre levels. What ion concentration are you aiming for? Is that a reasonable concentration?

Kind regards,

> On 6 Jan 2017, at 07:05, Raag Saluja <saluja.raag at gmail.com> wrote:
> Hi!
> 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
> 84300
> 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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