Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 250000 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to calculate the velocity autocorrelation using gmx velacc of those water molecules within 0.5nm of the protein. b) The orientation of those water molecules using the dipole of water using gmx h2order c) The tetrahedral order parameter for those particular water molecules how should I use the index file? Please provide me with the command and the process of calculation. Thanks and regards- Soham -- Gromacs Users mailing list
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