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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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