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Dear experts in the field,<div><br></div><div>When we use cosine content to determine if our simulation are converged or not, should I </div><div><br></div><div>(1) sum all the first three principal components together or examine individually?</div><div><br></div><div>(2) If I expect the first 10 ns is the equilbrium period, while the other 20 ns as the production period. Should I include all 30 ns of trajectory to the analysis or should I just include the last 20 ns trajectory to the analysis?</div><div><br></div><div>(3) Let's if I got the PC1 as low as 0.3, can I still claim the trajectories are converged?</div><div><br></div><div>(4) Did you comes across that when you increase the simulation time, the cosine content values of the first three principal components did not goes down but increased?</div><div><br></div><div>Best regards and many thanks for your comments and helpppppppp,</div><div><br></div><div>Catherine</div><div>New learner of Gromacs.<br><br><div
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