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GMX-HBOND-LEGACY(1)		     GROMACS		     GMX-HBOND-LEGACY(1)

NAME
     gmx-hbond-legacy - Compute and analyze hydrogen bonds

SYNOPSIS
	gmx hbond-legacy [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
		     [-num [<.xvg>]] [-g [<.log>]] [-ac [<.xvg>]]
		     [-dist [<.xvg>]] [-ang [<.xvg>]] [-hx [<.xvg>]]
		     [-hbn [<.ndx>]] [-hbm [<.xpm>]] [-don [<.xvg>]]
		     [-dan [<.xvg>]] [-life [<.xvg>]] [-nhbdist [<.xvg>]]
		     [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
		     [-xvg <enum>] [-a <real>] [-r <real>] [-[no]da]
		     [-r2 <real>] [-abin <real>] [-rbin <real>] [-[no]nitacc]
		     [-[no]contact] [-shell <real>] [-fitstart <real>]
		     [-fitend <real>] [-temp <real>] [-dump <int>]
		     [-max_hb <real>] [-[no]merge] [-acflen <int>]
		     [-[no]normalize] [-P <enum>] [-fitfn <enum>]
		     [-beginfit <real>] [-endfit <real>]

DESCRIPTION
     gmx  hbond-legacy	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  us-
     ing  -noda).  OH and NH groups are regarded as donors, O is an acceptor al-
     ways, 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  379:55, 1996; J. Chem. Phys.
     113:23, 2000).  If contact kinetics are analyzed by using the -contact  op-
     tion, then n(t) can be defined as either all pairs that are not within con-
     tact  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.

     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 he-
	  lices in proteins.

	* -hbn:  all selected groups, donors, hydrogens and  acceptors	for  se-
	  lected  groups, all hydrogen bonded atoms from all groups and all sol-
	  vent atoms involved in insertion. Output is limited unless -nomerge is
	  set.

	* -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 com-
	  pare results to Raman Spectroscopy.

     Note: options -ac, -life, -hbn and -hbm require an amount of memory propor-
     tional to the total numbers of donors times the total number  of  acceptors
     in the selected group(s).

OPTIONS
     Options to specify input files:

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -s [<.tpr>] (topol.tpr)
	    Portable xdr run input file

     -n [<.ndx>] (index.ndx) (Optional)
	    Index file

     Options to specify output files:

     -num [<.xvg>] (hbnum.xvg)
	    xvgr/xmgr file

     -g [<.log>] (hbond.log) (Optional)
	    Log file

     -ac [<.xvg>] (hbac.xvg) (Optional)
	    xvgr/xmgr file

     -dist [<.xvg>] (hbdist.xvg) (Optional)
	    xvgr/xmgr file

     -ang [<.xvg>] (hbang.xvg) (Optional)
	    xvgr/xmgr file

     -hx [<.xvg>] (hbhelix.xvg) (Optional)
	    xvgr/xmgr file

     -hbn [<.ndx>] (hbond.ndx) (Optional)
	    Index file

     -hbm [<.xpm>] (hbmap.xpm) (Optional)
	    X PixMap compatible matrix file

     -don [<.xvg>] (donor.xvg) (Optional)
	    xvgr/xmgr file

     -dan [<.xvg>] (danum.xvg) (Optional)
	    xvgr/xmgr file

     -life [<.xvg>] (hblife.xvg) (Optional)
	    xvgr/xmgr file

     -nhbdist [<.xvg>] (nhbdist.xvg) (Optional)
	    xvgr/xmgr file

     Other options:

     -b <time> (0)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit ps)

     -tu <enum> (ps)
	    Unit for time values: fs, ps, ns, us, ms, s

     -xvg <enum> (xmgrace)
	    xvg plot formatting: xmgrace, xmgr, none

     -a <real> (30)
	    Cutoff angle (degrees, Hydrogen - Donor - Acceptor)

     -r <real> (0.35)
	    Cutoff radius (nm, X - Acceptor, see next option)

     -[no]da (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 (yes)
	    Regard nitrogen atoms as acceptors

     -[no]contact (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

     -fitend <real> (60)
	    Time (ps) to which to stop fitting the correlation functions in  or-
	    der  to obtain the forward and backward rate constants for HB break-
	    ing and formation (only with -gemfit)

     -temp <real> (298.15)
	    Temperature (K) for computing the Gibbs energy corresponding  to  HB
	    breaking and reforming

     -dump <int> (0)
	    Dump the first N hydrogen bond ACFs in a single .xvg file for debug-
	    ging

     -max_hb <real> (0)
	    Theoretical maximum number of hydrogen bonds used for normalizing HB
	    autocorrelation  function.	Can  be useful in case the program esti-
	    mates it wrongly

     -[no]merge (yes)
	    H-bonds between the same donor and acceptor, but with different  hy-
	    drogen are treated as a single H-bond. Mainly important for the ACF.
	    Not compatible with options that depend on knowing a specific hydro-
	    gen: -noad, -ang.

     -acflen <int> (-1)
	    Length of the ACF, default is half the number of frames

     -[no]normalize (yes)
	    Normalize ACF

     -P <enum> (0)
	    Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

     -fitfn <enum> (none)
	    Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

     -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

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026		     GMX-HBOND-LEGACY(1)
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