Main Table of Contents

Thu 26 Aug 2010


g_dih can do two things. The default is to analyze dihedral transitions by merely computing all the dihedral angles defined in your topology for the whole trajectory. When a dihedral flips over to another minimum an angle/time plot is made.

The opther option is to discretize the dihedral space into a number of bins, and group each conformation in dihedral space in the appropriate bin. The output is then given as a number of dihedral conformations sorted according to occupancy.


-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Run input file: tpr tpb tpa
-o hello.out Output Generic output file

Other options

-[no]h gmx_bool no Print help info and quit
-[no]version gmx_bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w gmx_bool no View output xvg, xpm, eps and pdb files
-[no]sa gmx_bool no Perform cluster analysis in dihedral space instead of analysing dihedral transitions.
-mult int -1 mulitiplicity for dihedral angles (by default read from topology)