[gmx-users] B-factor calculations

Jon Ellis jon.ellis at utoronto.ca
Tue Jun 13 23:55:36 CEST 2006

Hello users

I am using B-factors to look at protein flexibility, using g_rmsf. I  
have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I  
did g_rmsf on the complex using the -oq option to obtain the bfac.pdb  
file, which gives me the B-factors averaged over the entire  
trajectory (I think).

Is it reasonable and physically valid to calculate b-factors varying  
over time, say by computing g_rmsf for smaller segments of my  
trajectory? If so, what would be a reasonable time interval for the  

Thanks in advance for your help


Jon Ellis
PhD Candidate, Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
Lash Miller 147
(416) 978-6568
jon.ellis at utoronto.ca

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