Gromacs
how to calculate Torsional angles χ1 and χ2 of a residue from gromacs MD run? which specific command?
You can use the g_angle tool:
g_angle -f -ov -all -n -type dihedral
You have to prepare an index file with quadruples of atoms constituting a dihedral. The following link describes which atoms to select:
http://www.msg.ucsf.edu/local/programs/garlic/commands/dihedrals.html
The first column of the output file contains the average of all dihedrals, the following columns contain individual dihedrals in the order given in the index file.
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