[gmx-users] Stress-Strain curve plot

[Mark Abraham]

Hi,

On Tue, 28 May 2019 at 23:26, Anh Vo <atv55 at msstate.edu> wrote:

> 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?
>

Pressure is a macroscopic quantity, and fluctutates more on short time
scales and over small numbers of particles. Usually there is a mismatch in
expectations that it fluctuates in the same manner as e.g. temperature.


> 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?
>

That depends on the models used. It might not be known that they are
capable of producing the right yielding 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?
>

Good question. I don't know if those are relevant things to verify. Is
there knowledge e.g. in the LAMMPS community of practice?


> 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?
>

When there are multiple pieces of hardware, GROMACS has to distribute the
work across them. Such errors indicate that the changes over time are
larger than might be expected in equilibrium (or near equilibrium)
simulations, which is what the implementations in GROMACS target. What
simulations produced such messages?

Mark

Thank you very much for sharing your time.
>
>
> Sincerely,
>
> Anh Vo
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