[gmx-users] GROMACS automation

[Mohamed Abdelaal]

I want to insert an atom with a velocity moving downwards toward the
graphene sheet in my box.
Yes I need to remove any atom moving away from my substrate or the
deposited atoms and far by 0.4 nm.
Then repeat the process until I have inserted 3000 atoms.

Thanks for your reply.
Mohamed

On Wed, Mar 11, 2020 at 13:43 John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> Write a script that calls gmx insert-molecules 3000 times and uses the
> previous output as input for each call.
>
>
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html
>
> Is there something you have to do in between each insertion?
>
> - John
>
> > Hello everybody,
> >
> > I am trying to insert molecules into a box but I have to insert one
> single
> > molecule at a time reaching 3000 molecule in total. Is there a way to
> > automate this process ?
> >
> > Thanks
> > Mohamed
> > --
> > 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.
> >
>
>
> --
> 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.
>