Main Table of Contents

Mon 2 Dec 2013


g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined based on cutoffs for the angle Hydrogen - Donor - Acceptor (zero is extended) and the distance Donor - Acceptor (or Hydrogen - Acceptor using -noda). 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.

With option -ac, rate constants for hydrogen bonding can be derived with the model of Luzar and Chandler (Nature 394, 1996; J. Chem. Phys. 113:23, 2000) or that of Markovitz and Agmon (J. Chem. Phys 129, 2008). If contact kinetics are analyzed by using the -contact option, then n(t) can be defined as either all pairs that are not within contact distance r at time t (corresponding to leaving the -r2 option at the default value 0) or all pairs that are within distance r2 (corresponding to setting a second cut-off value with option -r2). See mentioned literature for more details and definitions.

[ 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.

-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 useful 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. Index file
-num hbnum.xvg Output xvgr/xmgr file
-g hbond.log Output, Opt. Log 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
-don donor.xvg Output, Opt. xvgr/xmgr file
-dan danum.xvg Output, Opt. xvgr/xmgr file
-life hblife.xvg Output, Opt. xvgr/xmgr file
-nhbdist nhbdist.xvg Output, Opt. xvgr/xmgr file

Other options

-[no]h bool no Print help info and quit
-[no]version 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)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-a real 30 Cutoff angle (degrees, Hydrogen - Donor - Acceptor)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)
-[no]da bool yes 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)
-[no]nitacc bool yes Regard nitrogen atoms as acceptors
-[no]contact bool no Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
-shell real -1 when > 0, only calculate hydrogen bonds within # nm shell around one particle
-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 and formation. With -gemfit we suggest -fitstart 0
-fitstart real 1 Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with -gemfit)
-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/τ)
-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 it wrongly
-[no]merge bool yes H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
-geminate enum none Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details.: none, dd, ad, aa or a4
-diff real -1 Dffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd.
-acflen int -1 Length of the ACF, default is half the number of frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many 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 until the end

Known problems