g_hbond(1)

1g_hbond(1)                GROMACS suite, VERSION 4.5                g_hbond(1)
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NAME

6       g_hbond - computes and analyzes hydrogen bonds
7
8       VERSION 4.5
9

SYNOPSIS

11       g_hbond  -f  traj.xtc  -s  topol.tpr  -n  index.ndx  -num  hbnum.xvg -g
12       hbond.log -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx  hbhelix.xvg
13       -hbn  hbond.ndx  -hbm  hbmap.xpm  -don  donor.xvg  -dan danum.xvg -life
14       hblife.xvg -nhbdist nhbdist.xvg -[no]h -[no]version -nice int  -b  time
15       -e  time -dt time -xvg enum -a real -r real -[no]da -r2 real -abin real
16       -rbin real -[no]nitacc -[no]contact -shell real  -fitstart  real  -fit‐
17       start  real  -temp  real -smooth real -dump int -max_hb real -[no]merge
18       -geminate enum -diff real -acflen int  -[no]normalize  -P  enum  -fitfn
19       enum -ncskip int -beginfit real -endfit real
20

DESCRIPTION

22       g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are deter‐
23       mined based on cutoffs for the angle Acceptor - Donor - Hydrogen  (zero
24       is  extended)  and  the distance Hydrogen - Acceptor.  OH and NH groups
25       are regarded as donors, O is an acceptor always, N is  an  acceptor  by
26       default,  but this can be switched using  -nitacc. Dummy hydrogen atoms
27       are assumed to be connected to the first preceding non-hydrogen atom.
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29
30       You need to specify two groups for analysis, which must be either iden‐
31       tical or non-overlapping. All hydrogen bonds between the two groups are
32       analyzed.
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35       If you set -shell, you will be asked  for  an  additional  index  group
36       which  should  contain  exactly  one  atom. In this case, only hydrogen
37       bonds between atoms within the shell distance from  the  one  atom  are
38       considered.
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40
41        [ selected ]
42
43            20    21    24
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45            25    26    29
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47             1     3     6
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50
51       Note  that  the  triplets  need  not  be  on separate lines.  Each atom
52       triplet specifies a hydrogen bond to be analyzed,  note  also  that  no
53       check is made for the types of atoms.
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55
56        Output:
57
58        -num:  number of hydrogen bonds as a function of time.
59
60         -ac:    average  over all autocorrelations of the existence functions
61       (either 0 or 1) of all hydrogen bonds.
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63        -dist: distance distribution of all hydrogen bonds.
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65        -ang:  angle distribution of all hydrogen bonds.
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67        -hx:   the number of n-n+i hydrogen bonds as a function of time  where
68       n  and  n+i  stand  for residue numbers and i ranges from 0 to 6.  This
69       includes the n-n+3, n-n+4 and  n-n+5  hydrogen  bonds  associated  with
70       helices in proteins.
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72         -hbn:   all  selected  groups,  donors,  hydrogens  and acceptors for
73       selected groups, all hydrogen bonded atoms from all groups and all sol‐
74       vent atoms involved in insertion.
75
76         -hbm:   existence matrix for all hydrogen bonds over all frames, this
77       also contains information on solvent  insertion  into  hydrogen  bonds.
78       Ordering is identical to that in  -hbn index file.
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80         -dan:  write out the number of donors and acceptors analyzed for each
81       timeframe. This is especially useful when using  -shell.
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83        -nhbdist: compute the number of HBonds per hydrogen in order  to  com‐
84       pare results to Raman Spectroscopy.
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86
87       Note: options  -ac,  -life,  -hbn and  -hbm require an amount of memory
88       proportional to the total numbers of donors times the total  number  of
89       acceptors in the selected group(s).
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FILES

92       -f traj.xtc Input
93        Trajectory: xtc trr trj gro g96 pdb cpt
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95       -s topol.tpr Input
96        Run input file: tpr tpb tpa
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98       -n index.ndx Input, Opt.
99        Index file
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101       -num hbnum.xvg Output
102        xvgr/xmgr file
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104       -g hbond.log Output, Opt.
105        Log file
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107       -ac hbac.xvg Output, Opt.
108        xvgr/xmgr file
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110       -dist hbdist.xvg Output, Opt.
111        xvgr/xmgr file
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113       -ang hbang.xvg Output, Opt.
114        xvgr/xmgr file
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116       -hx hbhelix.xvg Output, Opt.
117        xvgr/xmgr file
118
119       -hbn hbond.ndx Output, Opt.
120        Index file
121
122       -hbm hbmap.xpm Output, Opt.
123        X PixMap compatible matrix file
124
125       -don donor.xvg Output, Opt.
126        xvgr/xmgr file
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128       -dan danum.xvg Output, Opt.
129        xvgr/xmgr file
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131       -life hblife.xvg Output, Opt.
132        xvgr/xmgr file
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134       -nhbdist nhbdist.xvg Output, Opt.
135        xvgr/xmgr file
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137

OTHER OPTIONS

139       -[no]hno
140        Print help info and quit
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142       -[no]versionno
143        Print version info and quit
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145       -nice int 19
146        Set the nicelevel
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148       -b time 0
149        First frame (ps) to read from trajectory
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151       -e time 0
152        Last frame (ps) to read from trajectory
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154       -dt time 0
155        Only use frame when t MOD dt = first time (ps)
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157       -xvg enum xmgrace
158        xvg plot formatting:  xmgrace,  xmgr or  none
159
160       -a real 30
161        Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
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163       -r real 0.35
164        Cutoff radius (nm, X - Acceptor, see next option)
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166       -[no]dayes
167        Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
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169       -r2 real 0
170        Second cutoff radius. Mainly useful with -contact and -ac
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172       -abin real 1
173        Binwidth angle distribution (degrees)
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175       -rbin real 0.005
176        Binwidth distance distribution (nm)
177
178       -[no]nitaccyes
179        Regard nitrogen atoms as acceptors
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181       -[no]contactno
182        Do  not  look  for  hydrogen bonds, but merely for contacts within the
183       cut-off distance
184
185       -shell real -1
186        when  0, only calculate hydrogen bonds within   nm  shell  around  one
187       particle
188
189       -fitstart real 1
190        Time  (ps)  from  which  to start fitting the correlation functions in
191       order to obtain the forward and backward rate constants for HB breaking
192       and formation. With -gemfit we suggest -fitstart 0
193
194       -fitstart real 1
195        Time  (ps) to which to stop fitting the correlation functions in order
196       to obtain the forward and backward rate constants for HB  breaking  and
197       formation (only with -gemfit)
198
199       -temp real 298.15
200        Temperature  (K)  for  computing  the Gibbs energy corresponding to HB
201       breaking and reforming
202
203       -smooth real -1
204        If = 0, the tail of the ACF will be smoothed by fitting it to an expo‐
205       nential function: y = A exp(-x/tau)
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207       -dump int 0
208        Dump the first N hydrogen bond ACFs in a single xvg file for debugging
209
210       -max_hb real 0
211        Theoretical  maximum  number of hydrogen bonds used for normalizing HB
212       autocorrelation function. Can be useful in case the  program  estimates
213       it wrongly
214
215       -[no]mergeyes
216        H-bonds between the same donor and acceptor, but with different hydro‐
217       gen are treated as a single H-bond. Mainly important for the ACF.
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219       -geminate enum none
220        Use reversible geminate recombination for the  kinetics/thermodynamics
221       calclations.  See  Markovitch  et al., J. Chem. Phys 129, 084505 (2008)
222       for details.:  none,  dd,  ad,  aa or  a4
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224       -diff real -1
225        Dffusion coefficient to use in the rev. gem. recomb. kinetic model. If
226       non-positive, then it will be fitted to the ACF along with ka and kd.
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228       -acflen int -1
229        Length of the ACF, default is half the number of frames
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231       -[no]normalizeyes
232        Normalize ACF
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234       -P enum 0
235        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or
236       3
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238       -fitfn enum none
239        Fit function:  none,  exp,  aexp,   exp_exp,   vac,   exp5,   exp7  or
240       exp9
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242       -ncskip int 0
243        Skip N points in the output file of correlation functions
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245       -beginfit real 0
246        Time where to begin the exponential fit of the correlation function
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248       -endfit real -1
249        Time  where to end the exponential fit of the correlation function, -1
250       is until the end
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252

KNOWN PROBLEMS

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

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

KNOWN PROBLEMS

SEE ALSO