[gmx-users] Stress-Strain curve plot

[Anh Vo]

Hi,

Thank you very much for your answers. There are many questions that I have
searched online and looked up in GROMACS manual but still confused, so I
asked here. Your answers help to clarify them a lot for me. I really
appreciate it.

However, there are some questions that I'm still not very clear about them.
Please help me to understand them more if possible.

- When I simulated  an equilibrated bilayer membrane under deformation in
GROMACS and compared the stress-strain curve with previous results in
LAMMPS, I got lower yield stress and higher yield strain. I think this
means the phospholipid chains may not be as “grabby” toward one another or
the chains are not pulling away from one another as quickly.
Is this problem 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?

- In the production step when the membrane is being deform (equibiaxial
tension with equal deformation velocities in X and Y direction), GROMACS
produceed such error: "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".
Is the Domain Decomposition automatically set in GROMACS for running
simulation and how to avoid this problem?

Thank you very much.

Anh Vo


>>
>> -----Original Message-----
>>
>> Message: 6
>>
>> Date: Wed, 29 May 2019 01:00:55 +0200
>>
>> From: Mark Abraham <mark.j.abraham at gmail.com>
>>
>>
>>
>> Hi,
>>
>>
>>
>> On Tue, 28 May 2019 at 23:26, Anh Vo <atv55 at msstate.edu> wrote:
>>
>>
>>
>> > Hi all,
>>
>> >
>>
>> >
>>
>> > I am 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
>>
>