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Say we take the basic example of a PEG molecule (PolyEthylene Glycol). What is the fundamental physics for computing the Elastic Modulus or the Young's Modulus from the Molecular Dynamics (MD) Simulation perspective? Support your explanation with a suitable .mdp file

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  • $\begingroup$ Underlying physics principle is simple - by computing the components of the pressure of the box while you pull the box. $\endgroup$ Feb 13 at 13:02

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You can apply certain strains to the system by modifying the input structure, e.g. stretching one direction and fixing the other directions. After running MD, one can extract stress components. Keep in mind, that for NPT-ensemble the stress fluctuates around a constant value, so you should go for NVT-ensemble.
Do this for different values of strain, where the linear relationship between stress and strain holds (Hook's regime). The elastic constants $C_{ij}$ come from the slopes of stress-strain curves. Depending on the symmetry of your system, different strains have to be regarded to calculate all elastic constants.

One thing: Elastic moduli are polycrystal constants. Their definition through elastic constants holds for solid crystals of size $\geq\mu m$ with grains. You cannot apply e.g. definition by Voigt or Reuss. Maybe I miss the property you want to calculate for the molecule.

Best
Lukas

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  • $\begingroup$ The question is not answered. How do you do the above in GROMACS? $\endgroup$
    – Pranoy Ray
    May 3 at 21:37

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