[gmx-users] Calculation of young's modulus from stress-strain plot

[Alessandra Villa]

Hi,

On Thu, Nov 28, 2019 at 1:23 PM Pragati Sharma <pragati2325 at gmail.com>
wrote:

> Hello users,
>
> I am trying to plot stress-strain curve for natural rubber from NPT
> simulations using the "deform" option. Deform along x direction at 1 bar
> pressure. The parameters I gave in mdp file are:
>
> Pcoupl                   = Berendsen
> Pcoupltype             = semiisotropic
> tau_p                     = 2
> compressibility        = 0 4.5e-5 4.5e-5
> ref_p                       = 1   1    1
> deform                   = 0.01 0 0 0 0 0
>
> Q. Should I give six values to ref_P and compressibility also.
>


Semiisotropic: Pressure coupling which is isotropic in the x and y
direction, but different in the z direction. Two values each for
compressibility and ref-p are required, for x/y and z directions
respectively.

Anisotropic: values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy
components, respectively. When the off-diagonal compressibilities are set
to zero, a rectangular box will stay rectangular. Beware that anisotropic
scaling can lead to extreme deformation of the simulation box.

Best regards
Alessandra


Q. If I give 'anisotropic'  coupling, then the error is
> "ERROR 1: Pressure coupling incorrect number of values (I need exactly 6)"
> Should I give the next three values as zero or 1. OR I can just use
> semiisotropic coupling only.
>
> Thanks in advance!!
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