Pressure Scaling more than 1% and volume fluctuations

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GROMACS version: 2025.0
GROMACS modification: Yes/No
Hi all,

I am kind of new to molecular dynamics simulations and I am trying to create a coarse-grained model of a small molecule using Martini 3 force field. I’ve created the mapping and the CG structure and trajectory files. I’m simulating the molecule in vacuum (EM → NVT → NPT → 15 ns MD, dt = 20 fs). With Parrinello–Rahman barostat I get the warning: Pressure scaling more than 1%. This may mean your system
is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during
equilibration can lead to simulation instability, and is discouraged.
Even with the warnings, run completes. So I checked the total energy and volume plots to see if the system is equilibrated. My total energy plot shows stable oscillations around a constant mean (as expected), but the box volume keeps swinging throughout the 15 ns. Switching to the C-rescale barostat removes the warning but volume fluctuations persist.

So my questions are:

  1. In vacuum, is it expected that the box volume under NPT will continue to oscillate?
  2. How should I tune PR settings (compressibility, τₚ) or box setup to stabilize volume in vacuum or is the problem about the previous coarse-graining steps and not the mdp parameters? Can it be just because the bond and angle constraints are not well-defined yet?
  3. Any recommendations for barostat choice or alternative ensembles for single-molecule CG runs in vacuum?

Thanks for any insights!

2

You cannot have a barostat in vacuum.