g_hbond

VERSION 3.1
Thu 28 Feb 2002

Description

g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined based on cutoffs for the angle Donor - Hydrogen - Acceptor (zero is extended) and the distance Hydrogen - Acceptor. OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom.

You need to specify two groups for analysis, which must be either identical or non-overlapping. All hydrogen bonds between the two groups are analyzed.

If you set -shell, you will be asked for an additional index group which should contain exactly one atom. In this case, only hydrogen bonds between atoms within the shell distance from the one atom are considered.

It is also possible to analyse specific hydrogen bonds with -sel. This index file must contain a group of atom triplets Donor Hydrogen Acceptor, in the following way:

[ selected ] 20 21 24 25 26 29 1 3 6
Note that the triplets need not be on separate lines. Each atom triplet specifies a hydrogen bond to be analyzed, note also that no check is made for the types of atoms.

-ins turns on computing solvent insertion into hydrogen bonds. In this case an additional group must be selected, specifying the solvent molecules.

Output:
-num: number of hydrogen bonds as a function of time.
-ac: average over all autocorrelations of the existence functions (either 0 or 1) of all hydrogen bonds.
-dist: distance distribution of all hydrogen bonds.
-ang: angle distribution of all hydrogen bonds.
-hx: the number of n-n+i hydrogen bonds as a function of time where n and n+i stand for residue numbers and i ranges from 0 to 6. This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated with helices in proteins.
-hbn: all selected groups, donors, hydrogens and acceptors for selected groups, all hydrogen bonded atoms from all groups and all solvent atoms involved in insertion.
-hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file.
-da: write out the number of donors and acceptors analyzed for each timeframe. This is especially usefull when using -shell.

Files

option	filename	type	description
`-f`	`traj.xtc`	Input	Generic trajectory: xtc trr trj gro g96 pdb
`-s`	`topol.tpr`	Input	Generic run input: tpr tpb tpa
`-n`	`index.ndx`	Input, Opt.	Index file
`-g`	`hbond.log`	Output, Opt.	Log file
`-sel`	`select.ndx`	Input, Opt.	Index file
`-num`	`hbnum.xvg`	Output	xvgr/xmgr file
`-ac`	`hbac.xvg`	Output, Opt.	xvgr/xmgr file
`-dist`	`hbdist.xvg`	Output, Opt.	xvgr/xmgr file
`-ang`	`hbang.xvg`	Output, Opt.	xvgr/xmgr file
`-hx`	`hbhelix.xvg`	Output, Opt.	xvgr/xmgr file
`-hbn`	`hbond.ndx`	Output, Opt.	Index file
`-hbm`	`hbmap.xpm`	Output, Opt.	X PixMap compatible matrix file
`-da`	`danum.xvg`	Output, Opt.	xvgr/xmgr file

Other options

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-[no]X`	bool	`no`	Use dialog box GUI to edit command line options
`-nice`	int	`19`	Set the nicelevel
`-b`	time	`-1`	First frame (ps) to read from trajectory
`-e`	time	`-1`	Last frame (ps) to read from trajectory
`-dt`	time	`-1`	Only use frame when t MOD dt = first time (ps)
`-[no]ins`	bool	`no`	Analyze solvent insertion
`-a`	real	`60`	Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
`-r`	real	`0.25`	Cutoff radius (nm, Hydrogen - Acceptor)
`-abin`	real	`1`	Binwidth angle distribution (degrees)
`-rbin`	real	`0.005`	Binwidth distance distribution (nm)
`-[no]nitacc`	bool	`yes`	Regard nitrogen atoms as acceptors
`-shell`	real	`-1`	when > 0, only calculate hydrogen bonds within # nm shell around one particle