4
$\begingroup$

Cross-posted later on Reddit.

I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in GROMACS are below:

tcoupl                   = v-rescale
tc-grps                  = SOLID W_ION
tau_t                    = 1.0 1.0
ref_t                    = 298 298
Pcoupl                   = parrinello-rahman
Pcoupltype               = anisotropic
tau_p                    = 12.0  
compressibility          = 0.0 3e-4 3e-4 0.0 0.0 0.0
ref_p                    = 0.0 1.0 1.0 0.0 0.0 0.0
deform                   = 0.002 0 0 0 0 0

Stress is computed as negative of the pressure tensor $-P_{xx}$. I wonder if water will affect my results, as I believe the pressure is computed for the whole system. Previously, I used to pull one end of the model, keeping the other side fixed. Here, I am just pulling the box. Would water affect my results?

The methodology for measuring the Young modulus was taken from this work: Modi V, Karttunen AJ. Molecular Dynamics Simulations on the Elastic Properties of Polypropylene Bionanocomposite Reinforced with Cellulose Nanofibrils. Nanomaterials. 2022; 12(19):3379.

$\endgroup$
1
  • 1
    $\begingroup$ +1. I've sent this to Antti Karttunen (one of the authors on the paper that you mentioned). Hopefully your $50 doesn't go to waste! $\endgroup$ Commented Feb 21, 2023 at 3:39

1 Answer 1

1
$\begingroup$

I spoke with one of the authors of the paper that you cited.

He said that you had also emailed him, that he sent you an input file, and that the answer on Reddit was a good one. Unfortunately that answer seems to be removed now, if you remember any of it, please share in an answer to this question and I can remove this Community Wiki post.

$\endgroup$
1
  • $\begingroup$ A tool such as "unddit.com" can be used to recover it pretty easily it looks like. $\endgroup$ Commented Mar 1, 2023 at 9:28

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .