[gmx-users] Pressure outputs from gmx energy

[Justin Lemkul]

On 10/27/19 1:45 AM, Anh Vo wrote:
> 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?

"Pressure" is the total pressure, the rest are the components of the 
pressure tensor.

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

The calculation of pressure is described in the manual.

> 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)?

Everything is included in the calculation. Again, refer to the manual.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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