Dear All,
I did a MD for my system for 7ns. I check the rmsd and ETOT are almost constant after 2 ns. So, take 2to7ns as the productive period after equilibrium.
I did a clustering analysis on the productive MD stimulations trajectory, i.e. 2 to 7 ns.
The input files is as follows:
-----------------------------------------------------
trajin ../xxx.mdcrd.gz
rsm first :1-45.CA,:46-500.C1'
cluster out xxx representative pdb \
average pdb means clusters 5 rms .CA,C1'
------------------------------------------------------
After all 5 clusters's average structures were obtained, I also find a xxx.txt file
I found
Cluster 0: has 12 points, occurence 0.120, average-distance-to-centroid is 0.455100
Cluster 1: has 12 points, occurence 0.120, average-distance-to-centroid is 0.484351
Cluster 2: has 25 points, occurence 0.250, average-distance-to-centroid is 0.520670
Cluster 3: has 29 points, occurence 0.290, average-distance-to-centroid is 0.536362
Cluster 4: has 22 points, occurence 0.220, average-distance-to-centroid is 0.489196
My question is if I want to check the statistical criteria such as sum of squares regression / total sum of squares. What should I do?
How can I tell if the cluster0...cluster4 are similar or not?
Based on the results that I got so far, should I used any one of the cluster's average structure to draw conclusions? It seems to me that no predominant cluster were found, all the occurences is 0.1 to 0.2. Should I expect to see only one cluster have the highest occurences if the system is equilibrated.
Any golden rule regarding on when to use cluster's average structure and when to use the average structure from production period?
Best regards,
Cat
_________________________________________________________________
Hotmail: Trusted email with powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 26 2010 - 01:30:39 PDT
