On 2013-07-31 07:20, bipin singh wrote:
Hello All,
I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the output
gives a single cluster. Please let me know if I have not understood it
correctly.
It means everything is within 0.3 nm RMSD from each other. Maybe your
system is very stable or you did not simulate very long. You can use a
shorter cut-off.
I am appending the output below:
####################################################
Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm
Found 1 clusters
Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
######################################################
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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