[gmx-users] Why RMSFs of some protein chains in my system are unreasonably large?

[David van der Spoel]

Hu Zhongqiao wrote:
> Dear all,
>  
> I finish a 10-ns MD simulations for a system including 16 lysozyme 
> molecule chains, some solvents H2O molecules and 128 Cl- counter ions 
> under PBC. When I use the command to calculate the RMSF of residues as 
> follows:
>  
> g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 for groups)
>  
> The results showed that 3rd and 14the chain had RMSF 1.2-2nm, which is 
> obviously unreasonable. But compared with other chains, these 2 chains 
> have the basically same peak places. The difference is that RMSFs of 
> residues in these 2 chains are systematically much higher. Is there a 
> bug resulting in a systematic error or any other reasons? Any 
> suggestions are welcome. Thanks,
>  
> Zhongqiao Hu
> Dept of Chemical and Biomolecular Engineering
> National University of Singapore  
> 
> 
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are all the lysozymes treated as one protein? in that case it might be a 
PBC artifact. try doing the rmsf per molecule (by running the program 16 
times) and then overlaying the result.

are you trying to crystallize it?

-- 
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://folding.bmc.uu.se
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