[gmx-users] multiple ion species in a single structure.

Mark Abraham mark.j.abraham at gmail.com
Mon May 14 11:05:12 CEST 2018


If you're doing an operation in stages, then the output of the first phase
needs to contribute to the input for the second, e.g. make a new tpr.

Otherwise, we'll need more information about what output you got and why it
didn't match your expectations.


On Mon, May 14, 2018, 10:57 Anna Vernon <lappala.anna at gmail.com> wrote:

> dear all
> I am struggling to understand why I cannot add several ion species into
> one structure. I want certain numbers of K CL NA ions.
> I use the following commands:
> gmx genion -s ions.tpr -o x_solv_ions.gro -p topol.top -pname K -nname
> CL -nn 3 -np 2
> gmx genion -s ions.tpr -o x_solv_ions.gro -p topol.top -pname MG -np 5
> But this does not seem to be the right way of doing it.
> I am not sure why this is going wrong... Any help would be greatly
> appreciated. Many thanks in advance!
> With  best wishes,
> Anna
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