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I wish to run an umbrella sampling on my protein. I am following the “Umbrella Sampling Tutorial” provided here: Umbrella Sampling (mdtutorials.com)). The tutorial says that the center of mass of the protofibril will be placed at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12.
My question is: How is the center of mass calculated for the protofibril in the tutorial, and how do I correctly define the box dimension for my protein?
Just for checking, I tried calculating the center of mass of the protofibril using the CALCOM server. The COM coordinates obtained from the CALCOM server (for protofibril) are different from the coordinates mentioned in the MD tutorials.