[gmx-users] Result analysis of protein water

Deep kumar deepak.choubey86 at gmail.com
Fri Sep 8 18:30:52 CEST 2017

Hello All,

I have performed MD on a protein water for 10ns, protein with total 164
residues in two chains. I have got the result graphs of radius of gyration
and rmsd for both wild and mutant. Wanted to attach the graphs but could
not due to bytes limit. There is one residue mutation (M -> T) in the
protein. I am new to MD analysis. Could you please let me know how to know
if the mutation is causing any conformational change. I can look at the
trajectories obtained of wild and mutant type, but to make accurate
analysis I would need more information. Also, please do share with me how
can i do more analysis to see the effect of mutations. Please let me know
if I need to provide more information.

Thanks & Regards.

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