[gmx-users] (no subject)

[shakira shukoor]

Thanks christian for the detailed description.

On Mon, Feb 17, 2020 at 8:00 PM Christian Blau <blau at kth.se> wrote:

> 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?
> >
> >
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106