[gmx-users] Pressure outputs from gmx energy

[Anh Vo]

Hi everyone,

When I use gmx energy to extract pressure for stress calculation from .edr
file,
I see those options: 15.PRESSURE, ..., 33.PRESS-XX, 34.PRESS-XY,
35.PRESS-XZ, 36.PRESS-YX, 37.PRESS-YY, 38.PRESS-YZ, 39.PRESS-ZX,
40.PRESS-ZY, 41.PRESS-ZZ.

1. What is the relation/difference between PRESSURE and
PRESS-XX,...,PRESS-YY,...,PRESS-ZZ? Or how to calculate PRESSURE from other
options?

2. Does PRESSURE represent von Mises stress in the system? What is exactly
or what causes the pressure/stress that we can output?

3. If I have a phospholipid bilayer in water solvent (72 POPC molecules in
the solvent of 9400 H2O molecules), does the output pressure/stress include
the stress caused by the solvent (water molecules) or not? In other words,
which molecules are included for the pressure/stress calculations (both
bilayer and the water solvent, or just the bilayer)?

Thank you very much for your help.

Best regards,
Anh Vo