[gmx-users] multiple ion species in a single structure.
nedomacho at gmail.com
Mon May 14 11:08:35 CEST 2018
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.
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