[gmx-users] gmx cluster

[sun]

Hi Everyone
I performed a 10ns MD using Gromos 43a1 ff and obtained frames at 10ps interval. However, When i gave gmx cluster command, I obatined 661 clusters. Does this indicate my proteini is not stable? However When i viewed trajectory in VMD, it seems good with least fluctuations in structure of protein and RMSD plot is also not bad. When again, i performed 10ms Md of protein-ligand, the number of clusters increased to 710. Is that ok?  

With Regards
Suniba

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