Water flow through a nanopore

User discussions
1

GROMACS version: 2021.4
GROMACS modification: No

Hello,

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!
Geoffrey.

2

Hi,

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.

Regards,
Petter

3

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

4

Is it possible/usefull to submit a Merge Request of your code here: https://gitlab.com/gromacs/gromacs/-/merge_requests