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

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 15 05:50:58 CEST 2006

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 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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