Water flow through a nanopore

GROMACS version: 2021.4
GROMACS modification: No


I want to simulate the flow of water molecules through a nanopore under a pressure drop.
To apply the pressure drop, I would like to use the same technique as the one used in this paper or this one.

This one consists in applying an external force f to all the oxygen atoms contained in a slice of the tank such that \Delta P = n f/A where n is the number of atoms in this slice and A its cross-section.

Until now, I have managed to do this by modifying the source code of GROMACS but I wonder if it is not possible to do this with pull-cde? If so, could you tell me how to do it because I couldn’t manage to do it.

Thanks in advance!


unfortunately, AFAIK there’s (currently) no way for the pull code to select atoms located in specific regions. I’m doing similar simulations myself, and resorted to modifying the source code.


Okay, I see. Thanks Peter for your answer.
I will keep on tweaking the GROMACS source code then.