[gmx-users] How to define coordinates of protein and simulation box in the pulling simulation automatically?

[Hassan Aaryapour]

Dear Justin A. Lemkul,



How do you calculated the coordinates for center (3.280, 2.181, 2.4775) and
box dimensions 6.560 x 4.362 x 12 in Umbrella Sampling by the following
program:

gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12.

When I calculate the geometrical center by chimera or accelrys discover
studio for my protein complex, it was emerged from box edges. How to
resolve it by softwares (not manually)?



Best Regards

Hassan