Hello,
I am using the following commands to create a dodecahedron box. I want a dodecahedron box with a long y-axis. However, when I use box sizes such as 20 45 20 or 20 60 20, I end up with the same number of atoms, which means the box size does not change. How can I control the dodecahedron box size? I need a box with a long y-axis for pulling a protein along this axis, while x and z axes of 20 nm are acceptable. Additionally, I want to keep my protein at the top edge of the y-axis. I’ve tried using a cubic box, which works, but I want to experiment with a dodecahedron box to reduce the system size.
Here is the command I used:
gmx editconf -f clpb_traj1_50_rotated.gro -o _custom_box_.gro -c -box 20 45 20 -bt dodecahedron
Output of above command:
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 36805 atoms
Volume: 8734.14 nm^3, corresponds to roughly 3930300 electrons
No velocities found
system size : 13.057 15.374 13.608 (nm)
diameter : 16.489 (nm)
center :-13.372 3.091 18.381 (nm)
box vectors : 14.851 14.851 39.602 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :8734.14 (nm^3)
shift : 28.372 11.909-11.310 (nm)
new center : 15.000 15.000 7.071 (nm)
new box vectors : 20.000 20.000 20.000 (nm)
new box angles : 60.00 60.00 90.00 (degrees)
new box volume :5656.85 (nm^3)
Thanks