[gmx-users] Selecting water molecules within a nanotube

[Alessandra Villa]

Hi,


On Tue, Feb 4, 2020 at 9:19 AM RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> Hi Users.
>
> I am simulating a nanotube in water medium. The nanotube is aligned to the
> center of the box using gmx editconfig and solvate. But I want to remove
> the water molecules within the nanotube. How do I compute this ?
>
> I understand that you do not want the water molecules inside the nanotube.
To get a starting configuration with no water in nanotube you could
1) generate a index file with a group containing all atoms expect water
molecules inside the nanotube. To do that use  gmx select (for the synthax
look at
http://manual.gromacs.org/documentation/current/onlinehelp/selections.html)
2) generate a gro file (gmx editconf) selecting the desired group

Best regards
Alessandra




> Thank you
>
> --
> *Regards,*
> *Rahul *
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