[gmx-users] Scale Triclinic Box

[Salman Zarrini]

Hi Maryam,

The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I
am just not sure if it could handle a triclinic cell.
Since your unit cell is not that large, you even can use Avogadro or
ASE-gui which both are good molecule editors and visualizers.

Cheers,
Salman

On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi <maryam.sadeghi.90 at gmail.com>
wrote:

> Dear All,
>
> I need to scale the a and b parameters of a triclinic crystalline unit
> cell. When I use the editconf command, only the cell parameters are scaled
> while the coordinates of atoms are not remapped in the new cell.
>
> gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686
> 1.9724 -angles 90.00 126.91 90.00
>
> The unit cell consists of 4 polymer chains, each chain having 7 repeating
> (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds,
> 340 angles and 376 dihedrals.
>
> The original cell parameters are:
> a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91,
> gamma: 90.00
>
> Any suggestions how I can remap the coordinates (keeping the bonds and
> angles constant) together with scaling the box?
>
> Thanks,
> --
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