[gmx-users] b-factor

[Mark Abraham]

tangxuan wrote:
> Dear all,
>  I have got a pdb file by command g_rmsf and option -oq, and the content
> of the file is like this:

> Could you tell me which column should be the b-factor?

Google is your friend :-) Try "pdb file format"

> B-factor is the
> thermal deviation of the atom, and could you tell me how the gromacs
> gives the values of b-factor for each atom in detail?  

If you want to know what GROMACS does in detail, that's why the authors 
gave you the source code. There might be a literature source there, but 
I think this is more like textbook material, e.g. google "definition 
crystallographic b-factor"

Mark