[gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

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,