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

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.xv

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

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 f