[gmx-users] How to calculate the COM and box vectors in umbrella sampling

[Maziya Ibrahim]

Dear all,

I want to carry out umbrella sampling on a protein-ligand complex, that was
already subjected to regular MD simulation for a few nanoseconds.

How should I calculate the optimum pull distance and box size to be used?
Is there a default value that can be applied?
Also how to calculate the center of mass of the protein and the box vectors?

Any suggestions?