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

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 27 21:15:27 CET 2017


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.


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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