[gmx-users] Use of index file generated by gmx select

Soham Sarkar soham9038 at gmail.com
Sun May 26 09:12:56 CEST 2019

    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-

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