[gmx-users] How to define the sublayers in the simulation and update the list of molecules at t timeinterval

[Alex]

My first thought precisely. Have a sufficiently long "bulk" region above
that nanotube and via pull code apply constant force to a layer of water at
the top of that region, essentially creating a form of a piston. A more
explicit version of this would be an actual piston subject to pulling.
Also, LAMMPS provides better tools for doing such things.

Alex

On Mon, Feb 27, 2017 at 1:15 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You can't do any kind of dynamic updating of groups used for eg pulling. If
> you really need what you describe, then your only current option is to stop
> the simulation, run gmx select to generate new index groups and restart it.
> But I would consider alternatives, such as pushing (some of) the reservoir
> with the pull code.
>
> Mark
>
> On Mon, 27 Feb 2017 13:40 Rana Ali <ranadeepu2017 at gmail.com> wrote:
>
> > Dear GROMACS users,
> >    I am working on 'Desalination process with CNT based membranes',
> where I
> > want to apply pressure gradient across CNT channel. I have fixed CNT
> > channel in z direction. This CNT channel  is connected with NaCl solution
> > reservoir at top and fresh water reservoir at bottom. Now I want to
> apply a
> > constant force (in z direction) to the oxygen atoms of a subset of water
> > molecules in layers of 0.2nm thick, located at both end of simulation
> box.
> > Also, list of molecules in the subset is required to be updated in each
> at
> > 10 ps, which is different from time step.
> > However, I don't know how to define the sublayers in the simulation, like
> > group of oxygen atoms with z>3.0 and also I am unaware how to list of
> > molecules can be updated. It would be very kind if anyone can help me to
> > overcome this problem ?
> > With Thanks in Advance.
> > Pooja
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