[gmx-users] b-factor

[tangxuan]

Dear all,
 I have got a pdb file by command g_rmsf and option -oq, and the content
of the file is like this:
TITLE     Protein in water
REMARK    THIS IS A SIMULATION BOX
CRYST1  148.918  148.918  148.428  59.89  59.89  90.00 P 1           1
MODEL        1
ATOM  47354  CA  ALA I9967      60.915  88.765  42.075  1.00 92.09
ATOM  47364  CA  GLY I9968      60.037  91.017  39.099  1.00 31.09
ATOM  47371  CA  PHE I9969      59.892  94.727  38.149  1.00 13.34
ATOM  47391  CA  LYS I9970      56.778  96.973  38.146  1.00 13.59
ATOM  47413  CA  ALA I9971      57.412 100.730  38.292  1.00  8.88
ATOM  47423  CA  GLY I9972      55.243 102.910  40.429  1.00  8.42
ATOM  47430  CA  VAL I9973      55.349 104.629  43.777  1.00  6.96
ATOM  47446  CA  LYS I9974      55.039 102.584  47.023  1.00 10.56
ATOM  47468  CA  ASP I9975      53.919 102.844  50.642  1.00  8.59
ATOM  47480  CA  TYR I9976      56.618 101.675  53.096  1.00  5.41
ATOM  47501  CA  ARG I9977      54.179 100.074  55.607  1.00  6.66
ATOM  47525  CA  LEU I9978      53.642  97.083  53.329  1.00 10.59
ATOM  47544  CA  THR I9979      57.043  95.266  53.147  1.00 10.24
ATOM  47558  CA  TYR I9980      59.307  96.919  55.730  1.00  4.74
ATOM  47579  CA  TYR I9981      57.141  96.770  58.853  1.00  4.52
ATOM  47600  CA  THR I9982      57.423  93.001  59.524  1.00  5.61
ATOM  47613  CA  PRO I9983      55.634  91.722  62.707  1.00 11.23
ATOM  47628  CA  ASP I9984      56.655  88.019  62.809  1.00 13.38
ATOM  47640  CA  TYR I9985      60.439  88.728  62.349  1.00  9.58
Could you tell me which column should be the b-factor? B-factor is the
thermal deviation of the atom, and could you tell me how the gromacs
gives the values of b-factor for each atom in detail?  

Thank you!


Tang Jiaowei