Gmx gyrate for the analysis of multi-model pdb file

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1

GROMACS version:2019
GROMACS modification: No
Hello,
I am using gmx gyrate to calculate radius of gyration of the ensemble of snapshots from docking output, written in multi-model format. The utility well recognizes the input format of my pdb and makes calculations. However there is a problem of the opening of the graph using xmgrace: since the TIME column is always zero, all the values of the first column are 0 and the graph looks like a vertical line. Is it possible to add some option to gmx gyrate in order to automatically number the values in the 1st column (e.g from 1 to 20, in the case when there are 20 models in my multi-model pdb file)?

2

gmx trjconv using -timestep on the input PDB file first before processing?

Other options are:

  • add values manually after processing, to the output .xvg file
  • import into other software add the values then export again i.e. Excel, use formula to input values, then export again and then plot with what ever plotting software you use.
  • tell your plotting software to plot the x axis as a category, not a numerical value.
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