Hi Peter,

Thank you so much for your fast reply. Changing from MDAnalysis to MDTraj for centering the Trajectory was the best idea and solved my issue.

I should have done it earlier.

Hi everyone, I love OpenMM but I am struggeling with one issue. I hope to get some input here: I am using MDAnalysis to analyze my trajectories. I have noticed that if I prepare everything with amber and run OpenMM from the prmtop and crd file, I am able to center my protein in the center of the wat...