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

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Fri Sep 15 04:02:46 CEST 2006

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
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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