[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


Hi,

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.

Mark

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
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list