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

Rana Ali ranadeepu2017 at gmail.com
Mon Feb 27 13:40:24 CET 2017

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.

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