[gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

Hi Salman,

Tnx for the info, I actually want to do the cold-compression on my
crystalline structure. So basically I need to both compress and expand the
a and b parameters of the unit cell (the c parameter is already
optimized)... so it's not just building a supercell, but rather scaling
only 2 parameters of the unit cell simultaneously while remaping the new
coordinates inside the scaled cell... could "gmx  genconf -nbox ... ...
..." handle this?

Best
Maryam


On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini <salman.zarrini at gmail.com>
wrote:

> 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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