[gmx-users] gmx cluster

sun sun.iba2 at gmail.com
Sun Feb 14 19:32:13 CET 2016

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

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