GROMACS version: 2021
GROMACS modification: Yes
During running an NVT simulation with xy-axes PBC box with two solid walls I came across an issue. I once got a different result when I accidentally set an incorrect size of the box in the gro file on the z-axis. Here are the snapshots which I got for my NVT simulations:
With the correct box size:
With an incorrect box size (you can see the boundary with the white border):
Is this an expected behavior? Is this because gromacs uses the box coordinates for the thermostat or there is another reason? Do you consider writing a warning message to the log file if in the input gro file there are atoms outside of the box? I hope you find this helpful as well. Thank you!
NVT.mdp (1.5 KB)