[gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

Hi Justin,
I actually want to scale the box (both moving the chains apart and close to
each other by changing the a and b parameters of the cell). I don't want to
run any dynamics at this point as I have already done quantum mechanics
minimization on this structure. When I use the editconf command the cell
parameters change but the coordinates of the atoms remain unchanged, i.e.
by compression the polymer chains remain outside of the cell... I was
wondering if editconf could scale the coordinates proportionally with the
cell parameters without distorting the bonds lengths?

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 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

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.

Best
Maryam




On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/3/20 11:16 PM, Maryam Sadeghi wrote:
> > 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?
>
> It sounds like you need to actually perform a simulation in which high
> pressure is applied to compress the box. genconf is for duplicating a
> box N times in each dimension, and while you can change box vectors and
> scale coordinates with editconf (-scale option), this is not the same as
> compressing them and bond lengths, etc. will become distorted.
>
> -Justin
>
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