Young's Modulus

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1

GROMACS version: 2023
GROMACS modification: Yes/No
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I have problem to analyse some mechanical property like modul young analysis. I do AA and CG for F-ACTIN protein and it’s about 1 year I couldn’t get any mechanical property analysis.
In young’s modulus, I used 2 ways:

  1. I used deformation dashboard in .mdp file, and applied stress in my box by displacement of simulation box in Z-direction, so after, I get Vir-ZZ and P-ZZ with (gmx energy) command as stress, and determine displacement of protein rather than initial length as strain. So I got stress-strain curve (and slope of initial region of it as young modulus), but it wasn’t true because the amounts were too high.
    I repeated simulation without water but it was un-acceptable amount too, and also changed velocity of box displacement, and do position restrain for initial monomer of protein but all of these changes weren’t true!!!
    This track is unclear for me right now.

  2. I pulled the final monomer of my molecule and restrain of initial monomer with (constant force or constant rate) states, and finally got Force-Displacement curve, that slope of it becomes constant in bellow formula:

Modul young = K × (initial length/area of ​​polymer)

By that formula I got young module but it was completely incorrect too.

Could you please help me to drive true value of options and tracks, and finally detemine true value of young modul?

2

There are many potential issues here.

The first thing I would like to say is that you should use the GROMACS 2024 release, as the deform option has been improved for, in particular for cases like this. This might or might not make a difference.

The second thing is that one has to use a low enough stress or strain rate. Molecular time scales are very fast, so often extremely long simulation are required to reach low enough strain rates.

Another issue could be unit conversions.