How do we omit the positive/negative strain at zero stress?

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1

GROMACS version: 2022

Hi All,

I have a polymer composite equilibrated using an annealing protocol. When I perform tensile MD simulation for the equilibrated structure, I get a high stress value at zero strain, and the Stress-strain curve does not start from (0,0). Please see the attached image for the stress-strain curve. for 2% strain. What can I do to avoid this? I aim to calculate the Young’s modulus from MD data. Appreciate your help.

Thank you.

image
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2

You need to work on your knowledge of fundamental physics. It doesn’t matter that your plot starts with negative stress, you can simply shift the origin in the strain axis to the point with zero stress. If you wanted to actually start simulating at zero stress, you should have done a proper NpT-equilibration first.