Dear All, I would like suggestions on the following questions in Essential Dynamics analysis. I have been working on the essential dynamics analysis of a 450 aa protein and its mutant.
To exclude the existance of random diffusion effects, I calculated cosine content and found it to be very high for the 1st principle component (~0.9), and very low (< 0.02) for subsequent PCs. Later to just check I did the same analysis using the starting structure as reference for g_covar. I found that the cosine content has dropped down to ~0.2 for the first PC. My question is why the cosine content is dependent on the fitting structure used in g_covar? And, especially, which structure is recommended to use in Essential Dynamics analysis of a combined trajectory? If we do have PCs with high cosine content, how should we interpret the results? Thankyou so much for your suggessions. kind regards, sridhar _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
