[gmx-users] Regarding gromos method in g_cluster

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se