[gmx-users] Uniaxial elongation using deform option

[Alessandra Villa]

Hi,
Some comments below. I hope they help you

On Mon, Jan 20, 2020 at 6:51 AM Pragati Sharma <pragati2325 at gmail.com>
wrote:

> Dear all,
>
> I want to calculate young's modulus of a polymer using uniaxial elongation.
> (elongation in z axis but no volume change)
> I am using 'deform' option and semiisotropic pressure coupling and zero
> compressibility in z for that.

My mdp parameters ar:
>
> *Pcoupl                   = BerendsenPcoupltype            =
> semiisotropictau_p                     = 1compressibility       = 4.5e-5
> 0


compressibility       = 4.5e-5 is  the compressibility for water solution.
Is this value also appropriate for the simulated system?



> ref_p                       = 1 1gen_vel                    = nogen_temp
>               = 298; options for non-eq viscosity calcdeform = 0 0 0.001 0
> 0 0refcoord_scaling = com*
>
>
Do you need refcoord_scaling? See for details
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=ref%20coord%20scaling#mdp-refcoord-scaling



> Since elongation is in z axis, Lz increases, and Lx and Ly decreases, but
> the decrease in these two axis is less compared to increase in Lz, and so
> my volume is not conserved, it is increasing.
>
>
The simulations are performed using the pressure coupling, thus controlling
the pressure.
I suggest to monitor the pressure along x and y to check if the simulation
setting are appropriate.
Are those values constant and at the desired values?



> Can anyone suggest me some way for uniaxial elongation in gromacs, but
> volume should not change
>
> Thanks!
>

Best regards
Alessandra



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