g_hbond - computes and analyzes hydrogen bonds
g_hbond -f traj.xtc -s topol.tpr -n index.ndx -num hbnum.xvg -g
hbond.log -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx hbhelix.xvg
-hbn hbond.ndx -hbm hbmap.xpm -don donor.xvg -dan danum.xvg -life
hblife.xvg -nhbdist nhbdist.xvg -[no]h -nice int -b time -e time -dt
time -[no]xvgr -[no]ins -a real -r real -[no]da -r2 real -abin real
-rbin real -[no]nitacc -[no]contact -shell real -fitstart real -temp
real -smooth real -dump int -max_hb real -[no]merge -acflen int
-[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
(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
You need to specify two groups for analysis, which must be either
identical or non-overlapping. All hydrogen bonds between the two groups
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
[ 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
-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.
-dan: write out the number of donors and acceptors analyzed for each
timeframe. This is especially usefull when using -shell.
-nhbdist: compute the number of HBonds per hydrogen in order to
compare results to Raman Spectroscopy.
Note: options -ac, -life, -hbn and -hbm require an amount of memory
proportional to the total numbers of donors times the total number of
acceptors in the selected group(s).
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input, Opt.
-num hbnum.xvg Output
-g hbond.log Output, Opt.
-ac hbac.xvg Output, Opt.
-dist hbdist.xvg Output, Opt.
-ang hbang.xvg Output, Opt.
-hx hbhelix.xvg Output, Opt.
-hbn hbond.ndx Output, Opt.
-hbm hbmap.xpm Output, Opt.
X PixMap compatible matrix file
-don donor.xvg Output, Opt.
-dan danum.xvg Output, Opt.
-life hblife.xvg Output, Opt.
-nhbdist nhbdist.xvg Output, Opt.
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)
Add specific codes (legends etc.) in the output xvg files for the
Analyze solvent insertion
-a real 30
Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
-r real 0.35
Cutoff radius (nm, X - Acceptor, see next option)
Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
-r2 real 0
Second cutoff radius. Mainly useful with -contact and -ac
-abin real 1
Binwidth angle distribution (degrees)
-rbin real 0.005
Binwidth distance distribution (nm)
Regard nitrogen atoms as acceptors
Do not look for hydrogen bonds, but merely for contacts within the
-shell real -1
when 0, only calculate hydrogen bonds within nm shell around one
-fitstart real 1
Time (ps) from which to start fitting the correlation functions in
order to obtain the forward and backward rate constants for HB breaking
-temp real 298.15
Temperature (K) for computing the Gibbs energy corresponding to HB
breaking and reforming
-smooth real -1
If = 0, the tail of the ACF will be smoothed by fitting it to an
exponential function: y = A exp(-x/tau)
-dump int 0
Dump the first N hydrogen bond ACFs in a single xvg file for debugging
-max_hb real 0
Theoretical maximum number of hydrogen bonds used for normalizing HB
autocorrelation function. Can be useful in case the program estimates
H-bonds between the same donor and acceptor, but with different
hydrogen are treated as a single H-bond. Mainly important for the ACF.
-acflen int -1
Length of the ACF, default is half the number of frames
-P enum 0
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
-fitfn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
-ncskip int 0
Skip N points in the output file of correlation functions
-beginfit real 0
Time where to begin the exponential fit of the correlation function
-endfit real -1
Time where to end the exponential fit of the correlation function, -1
is till the end
- The option -sel that used to work on selected hbonds is out of
order, and therefore not available for the time being.
More information about GROMACS is available at
Thu 16 Oct 2008 g_hbond(1)