Pressure is not going to 1 bar

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Dear Gromacs users
I am doing a protein-ligand simulation in which I was getting Lincs warning during the production run. To solve this I run longer energy minimizations and after nvt; I run npt in 2 steps first 500 ps at Berendsen and second 500ps at Parinello-Rahman
I am getting following values for pressure for the first equilibration:-

Energy Average Err.Est. RMSD Tot-Drift

Pressure -3.41278 3.7 73.0311 22.1736 (bar)

Statistics over 500001 steps [ 0.0000 through 500.0000 ps ], 1 data sets
All statistics are over 5001 points

For the second npt

Energy Average Err.Est. RMSD Tot-Drift

Pressure 0.702052 0.32 68.0829 0.180525 (bar)

The pressure did not reach to 1 bar yet. Should I run longer npt or it is sufficient for starting production run?
I need your valuable suggestions, please. I have attached npt.mdp files for your review and suggestions.
npt2.mdp (2.6 KB) npt.mdp (2.6 KB)
Thanks.
Sadaf

2

Hi sadaf,

The pressure can vary quite drastically during simulations, especially when you run a quite small system. On first sight, your .mdp file looks okay.

3

This topic gets discussed frequently, including within the last few days on this forum. Please refer to http://manual.gromacs.org/current/user-guide/terminology.html#fluctuation and ask yourself: is 0.7 ± 68 statistically different from the target value of 1?

4

Some examples to show you how much pressure can fluctuate, and how it is a factor of the number of atoms/particles in the simulation: https://twitter.com/dr_dbw/status/968624615063937025