GROMACS version: GROMACS/2021.3
GROMACS modification: No
I’ve encountered an issue with NVE for a system consisting of a single type of organic molecule (C24H10N2O4), which seems to be well equilibrated before running NVE. See the included figures for plots of the total system energy, pressure and temperature as a function of simulation length, where the different colored curves corresponds to the different parts of my simulation protocol. The system looks well equilibrated before NVE in my opinion, but as soon as I remove the thermostat/barostat the energy, pressure and temperature drifts.
I’ve tried decreasing the timestep in the NVE simulation to 0.05 fs, as well as run a longer NVE simulation without any luck. I also added an extra round of NVT (nvt_intermediate) before NVE as I read in another post on this forum that that would be beneficial.
Does anyone know what might be causing this behavior? Any tips or feedback on what I might try next is greatly appreciated!
Here is my simulation protocol in more detail:
- em (Energy minimization): steep
- nvt: tcoupl=v-rescale, tau-t=1, pcoupl=no, generate velocities at 400K
- npt_high_p: tcoupl=berendsen, tau-t=2.0, pcoupl=berendsen, tau-p=1, ref-p: 2000 bar (to fix cavitation in the system)
- npt: tcoupl=v-rescale, tau-t=2.0, pcoupl=Parinello-Rahman, tau-p=5, ref-p: 1 bar
- nvt_intermediate: v-rescale, tau-t=1, pcoupl=no
- nve_prod: tcoupl=no, pcoupl=no
Plot of energy during simulation
Plot of pressure during simulation
Plot of temperature during simulation