Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-hbond - Compute and analyze hydrogen bonds

SYNOPSIS

          gmx hbond [-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  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 379:55,  1996;  J.  Chem.  Phys.  113:23,  2000).   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.

       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 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).

OPTIONS

       Options to specify input files:

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

       -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 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

       -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 (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.

       -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

KNOWN ISSUES

       · The option -sel that used to work on selected hbonds is out of order, and therefore  not
         available for the time being.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team