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

Maziya Ibrahim maziya.ibrahim at gmail.com
Thu Jul 10 07:47:20 CEST 2014

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?

More information about the gromacs.org_gmx-users mailing list