[gmx-users] Calculate Young''s modulus using NPT and anisotropic
veerapandian
veera.pandi33 at gmail.com
Tue May 14 10:37:35 CEST 2019
Dear GROMACS members,
I would like to calculate the Young's modulus for crystalline cellulose.
I simulate the system using NPT ensemble with anisotropic barostat.
I apply a constant stress in a given direction. For instance, I apply a
constant stress in XX direction and set the compressability for this
direction is 0.0 (Is this correct?)
I have tried the following options,
pcoupl = berendsen
pcoupltype = anisotropic
ref_p = 100.0 1.0 1.0 1.0 1.0 1.0
compressibility = 0.0 2.2e-5 7.9e-7 1.2e-5 4.2e-5 4.4e-5
;compressibility = 2.5e-5 2.2e-5 7.9e-7 1.2e-5 4.2e-5 4.4e-5 (if I use
this option I get, Triclinic box is too skewed - Segmentation fault (core
dumped))
My idea is that after a few ns simulations (once the system has reached
equilibrium state), I will calculate the Young's modulus using the
following relation.
In the case of XX direction,
E (Young's modulus) = stress / strain = (-Pxx) / ((del Lxx - Lxx) / Lxx)
I am little confused with the gromacs input.
because I almost get the same Youngs modulus value when I apply a constant
stress in other directions as well (YY and ZZ).
Did I miss something in the gromacs input or in the formula.
Thanks in advance for you valuable suggestions.
Best regards,
Veera
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