g_dih

NAME

g_dih − analyzes dihedral transitions

SYNOPSIS

g_dih -f traj.xtc -s topol.tpr -o hello.out -[no]h -nice int -b time -e time -dt time -[no]w -[no]sa -mult int

DESCRIPTION

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.

FILES

-f traj.xtc Input
Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input
Generic run input: tpr tpb tpa xml

-o hello.out Output
Generic output file

OTHER OPTIONS

-[no]h no
Print help 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 no
View output xvg, xpm, eps and pdb files

-[no]sa no
Perform cluster analysis in dihedral space instead of analysing dihedral transitions.

-mult int -1
mulitiplicity for dihedral angles (by default read from topology)