[gmx-users] Stress-Strain curve plot

[Anh Vo]

Hi all,


I’m running GROMACS to simulate a simple phospholipid bilayer membrane
(POPC) under deformation, and plot the von Mises stress-strain curve to
determine yielding point.



I have got the membrane deformed and extractred output pressures from .edr
file (option PRESS X, PRESS Y, PRESS Z) to calculate the stress, then use
that calculated stress and true strain to plot the curve. The general shape
of the curve is correct; however, the pressure value fluctuates widely in
GROMACS and the yield stress/ yield strain is wrong. Why did I get the
wrong value and where/ which parameter files should I address to solve this
problem?


1. I got a lower yield stress and a higher yield strain than it should be
(compared to previous research findings on similar problem using LAMMPS).
Why did I get this problem, and what should I fix to get the right yielding
stress/strain values?

2.  Is the wrong value due to the incorrect bonding or constraint between
the molecules? If this is the case, which files or which parameters should
I look into to modify the bond or constraints? Does lower yield stress and
higher yield strain means that the bond in GROMACS is more ductile?


3.   Sometimes I run the same simulation several times without changing
anything to double check. I can get similar results most of the time, but
sometimes the simulation stop faster and an error is reported like this
“The domain decomposition grid has shifted too much in the Z-direction
around cell 0 0 3. This should not have happened. Running with fewer ranks
might avoid this issue”.

What does this error mean? What is domain decomposition? Is the Domain
Decomposition automatically set in GROMACS for running simulation?


Thank you very much for sharing your time.


Sincerely,

Anh Vo