Rmsf according to referans gro files

User discussions
1

GROMACS version: VERSION 5.1.4
GROMACS modification: No
I have ref_open and ref_closed files for MurD protein. I want to calculate rmsf of MurD_closed.gro with average. I thought gmx-rmsf command calculates average coordinates in the trajectory. But I got the different rmsf values when I used the different referans files. I used this codes :

  • gmx_mpi rmsf -f MurD_closed.gro -s ref_closed.gro -o rmsf_closed_refclosed.xvg
  • gmx_mpi rmsf -f MurD_closed.gro -s ref_open.gro -o rmsf_closed_refopen.xvg
    I tried -res and -fit flag but there is no difference between the values. Can you help me? Does anyone have any ideas on this subject? How can I calculate based on average? Thank you :)
2

RMSF is computed relative to the average coordinates over the trajectory. The reference structure in -s is used for least-squares fitting, if specified (which is the default behavior).