[gmx-users] (no subject)

[Christian Blau]

Hi Shakkira,


The simulation box deformation is described by six parameters that describe three basis box vectors with the following 
contraints,

  - the first box vector is aligned along the x-axis, with coordinates thus has coordinates (xx,0,0)

  - the second box vector is aligned in the x-y plane with coordinates (yx,yy,0)

  - the third box vector is free (zx,zy,zz)


The six parameters that you give in .mdp files are in the following order

xx, yy, zz, yx, zx, zy


The corrent box is then calculated as

box(t_start)+(t-t_start)*deform


For more information have a look at the gromacs manual mdp parameter description:

http://manual.gromacs.org/current/user-guide/mdp-options.html

under non-equilibrium MD:

    (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
    The velocities of deformation for the box elements: a(x) b(y) c(z)
    b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
    is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
    elements are corrected for periodicity. The coordinates are
    transformed accordingly. Frozen degrees of freedom are (purposely)
    also transformed. The time ts is set to t at the first step and at
    steps at which x and v are written to trajectory to ensure exact
    restarts. Deformation can be used together with semiisotropic or
    anisotropic pressure coupling when the appropriate
    compressibilities are set to zero. The diagonal elements can be
    used to strain a solid. The off-diagonal elements can be used to
    shear a solid or a liquid.


Best,

Christian

On 2020-02-16 12:12, shakira shukoor wrote:
>    Hi all
> Can anyone help me with the DEFORM option in Gromacs to change the box
> values?
>
>