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

[Alex]

Not sure if this got sent (I received a weird 'server busy' message 
here), but see below.


On 5/14/2018 3:06 AM, Alex wrote:
>
> Hi Anna,
>
> Indeed, genion requires the tpr generated with the previous set of 
> ions to add new species, so your approach won't work. Here's what 
> routinely works for me (using your own notation):
>
> gmx genion -s ions.tpr -o *x_solv_ions.gro* ............ (add first 
> set of ions)
>
> gmx grompp -f <some placeholder mdp> -c *x_solv_ions.gro* -p topol.top 
> .......... -o *ions1.tpr* (generate another tpr)
>
> gmx genion -s *ions1.tpr* ............... (add second set of ions)
>
> Your topol.top will be updated properly and you will have old topology 
> backups to verify that each step did exactly what you wanted.
>
> Cheers,
>
> Alex
>
>