Nvt equilibration in with walls

User discussions
1

GROMACS version: 2024.1
GROMACS modification: Yes/No
Hi,

I performed NVT equilibration of my system (Cu slab + aqueous solution of CO2) in xy plane. I imposed 2 walls at z=0 and z=z-box (nwall=2, wall potential: 9-3). After the simulation I viewed .gro and .trr in VMD and in the beginning the box size changes a bit in the z-direction. Almost like it was scaled or something. I don’t understand why because working in canonical ensemble the box volume should be constant. Maybe it has something to do with walls? I’ve never done anything with walls before so maybe it’s normal?

Kind regards,

simulatorkadimi

2

How did you see that the box size changed in VMD?

You can compare the box in your input structure file and confout.gro. They should be identical when using an NVT ensemble.