[gmx-users] What is an acceptable cosine content values?

a a patd_2 at hotmail.com
Thu Apr 12 11:24:52 CEST 2012

Dear experts in the field,
When we use cosine content to determine if our simulation are converged or not, should I 
(1) sum all the first three principal components together or examine individually?
(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?
(3) Let's if I got the PC1 as low as 0.3, can I still claim the trajectories are converged?
(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?
Best regards and many thanks for your comments and helpppppppp,
CatherineNew learner of Gromacs.

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