Provided by: gromacs-data_4.6.5-1build1_all bug


       g_hbond - computes and analyzes hydrogen bonds

       VERSION 4.6.5


       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 -[no]version -nice
       int -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 -fitstart real -temp
       real -smooth real -dump int -max_hb real -[no]merge -geminate enum -diff real -acflen  int
       -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real


         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

       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


        Print help info and quit

        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)

        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 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/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 it wrongly

        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

       -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

        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


       - 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 <>.

                                          Mon 2 Dec 2013                               g_hbond(1)