Hello everyone,
I have a large trajectory (60,000 frames) and am trying to perform a cluster analysis on it. I know that ptraj only has the capability of using 32,000 frames for each analysis, so I've done 4 cluster analyses for frames 1-15000, 15-30000, 30-45000, and 45-60000. Is this the right way to go about it? If so, how do I then compare the clusters I've gotten back to each other. I have the idea to do an RMSD of each of the pdb's but I'm not positive if that's correct. Basically, I'm looking for the most prominent structure in my trajectory file for further analysis.
Thanks,
Kira Armacost
Ph.D candidate
Auburn University
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Received on Thu Sep 27 2012 - 12:00:03 PDT
