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       g_hbond - computes and analyzes hydrogen bonds

       VERSION 4.0.1


       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
       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

       [ 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.
        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

       -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
       xmgrace program

        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
       cut-off distance

       -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
       and formation

       -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.

       -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

       -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)