[gmx-users] How to calculate the COM and box vectors in umbrella sampling
maziya.ibrahim at gmail.com
Thu Jul 10 07:47:20 CEST 2014
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?
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