gmx-hbond(1) GROMACS Manual gmx-hbond(1)NAMEgmx-hbond - Compute and analyze hydrogen bonds
SYNOPSIS
gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-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>]]
[-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>] [-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 iden‐
tical 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 (correspond‐
ing 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.
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 sol‐
vent 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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-num [<.xvg>] (hbnum.xvg) (Output)
xvgr/xmgr file
-g [<.log>] (hbond.log) (Output, Optional)
Log file
-ac [<.xvg>] (hbac.xvg) (Output, Optional)
xvgr/xmgr file
-dist [<.xvg>] (hbdist.xvg) (Output, Optional)
xvgr/xmgr file
-ang [<.xvg>] (hbang.xvg) (Output, Optional)
xvgr/xmgr file
-hx [<.xvg>] (hbhelix.xvg) (Output, Optional)
xvgr/xmgr file
-hbn [<.ndx>] (hbond.ndx) (Output, Optional)
Index file
-hbm [<.xpm>] (hbmap.xpm) (Output, Optional)
X PixMap compatible matrix file
-don [<.xvg>] (donor.xvg) (Output, Optional)
xvgr/xmgr file
-dan [<.xvg>] (danum.xvg) (Output, Optional)
xvgr/xmgr file
-life [<.xvg>] (hblife.xvg) (Output, Optional)
xvgr/xmgr file
-nhbdist [<.xvg>] (nhbdist.xvg) (Output, Optional)
xvgr/xmgr file
Other options:
-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, 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 esti‐
mates 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, vac, exp5, exp7, exp9, erf‐
fit
-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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-hbond(1)
