Box explodes using NPT.mdp

User discussions
, ,
1

GROMACS version: 2022
GROMACS modification: No
I performed a simulation (equilibration) with a Janus MoSSe box containing ions and water. However, my box explodes when I use NPT.mdp. I’m attaching the mdp inputs regarding 1-optimize (equilibration) and 2-NPT and along with some screenshots of the simulation visualization: 01 = when it starts, 02 = the box decrease, and 03 and 04 the box explodes. Could someone help, or suggest a way to fix this problem?

04
041071×869 149 KB

03
031051×876 220 KB

02
021087×880 323 KB

01
011064×869 398 KB

1-optmize.mdp (1.7 KB)

2-NPT.mdp (3.8 KB)

2

Hi, I would suggest using c-rescale and possibly reduce the compressibility by a factor of 10, at least in the equilibration phase. I think you can use a semiisotropic scaling instead of anisotropic for your setup.

3

Note that frozen atoms cause issues with the pressure calculation. I don’t know how large the effect is in your system, but this could make pressure coupling impossible to use.