gmx-hbond - Online in the Cloud

PROGRAM:

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 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.

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)
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)
Unit for time values: fs, ps, ns, us, ms, s

-xvg <enum>
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.

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