[gmx-users] Addition of ions in vacuum simulations

Mark Abraham mark.abraham at anu.edu.au
Thu Oct 18 08:49:15 CEST 2007

> Hi all,
> I am simulating a charged peptide in vacuum. I want to neutralize my
> system by using genion command,and as expected it asks me a continuous
> solvent group for the replacement; however, I have no solvents.
> How can I add ions to my system if I am in vacuum? or Is it necessary to
> add ions while performing simulations in vacuum?

This is a chemistry question that will depend on your protein and what
you're trying to study. In some cases you might also consider modifying
the chemical groups so that there is not an ion there.


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