gmx-hbond - Compute and analyze hydrogen bonds
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>]
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 to specify input files:
Options to specify output files:
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
- •
- The option -sel that used to work on selected hbonds is out of
order, and therefore not available for the time being.
gmx(1)
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