[gmx-users] bfactor

[David van der Spoel]

On Fri, 2004-05-14 at 11:46, smith wrote:
> hi all,
> I have certain queries to ask
> 
> I have completed md on a protein for ns.
> 
> 1.I want pdb files at say at every 25 ps interval with bfactors attached in the pdb files as u see in crystallographically solved structure.
> 
> 2.Actually I want to see variation in B-factors for the atoms during the period of simulation,like rmsd with respect to time.
>  
> BY using trjconv i got pdbfiles at desired time intervals,but bfactor variation how to get it,is there a option.
>  
> thanls for any suggestion.cheers -smith 
run g_rmsf with some flags
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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