[gmx-users] force application group wise

[Mark Abraham]

Hi,

gmx select will let you make index groups according to geometric criteria,
which will allow you to set up something like a piston of water. But of
course the molecules will diffuse, so you will want to periodically stop
the simulation, and re-build the index group for the next call to grompp.

Mark

On Tue, Mar 14, 2017 at 2:06 PM Rana Ali <ranadeepu2017 at gmail.com> wrote:

Dear Mark
Thanks for your response. Now I have understood. Next I have created a
layer of water molecules above a graphene layer. How I can make two groups
of water   say water at the topmost layer with 1.4nm thickness and rest of
the water molecules up to graphene surface.

Thanks in advance

Warm regards

On Fri, Mar 3, 2017 at 1:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is what pull groups do in GROMACS.
>
> Mark
>
> On Fri, 24 Feb 2017 14:37 Rana Ali <ranadeepu2017 at gmail.com> wrote:
>
> > Dear users
> >
> > We were running MD system consists of ion and water through a nanotube
> > under a pressure gradient.
> > For that we are applying pressure in terms of force to the molecules.
> > Could any body help how to create group so that the external force will
> be
> > applied only on water molecules not on the ions. means how to define the
> > force in the .mdp file
> >
> > Thanks in advance
> >
> > Warm regards
> >
> > Rana
> > --
> > 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.
>
--
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.