1GMX-HBOND(1)                        GROMACS                       GMX-HBOND(1)
2
3
4

NAME

6       gmx-hbond - Compute and analyze hydrogen bonds
7

SYNOPSIS

9          gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
10                    [-num [<.xvg>]] [-g [<.log>]] [-ac [<.xvg>]]
11                    [-dist [<.xvg>]] [-ang [<.xvg>]] [-hx [<.xvg>]]
12                    [-hbn [<.ndx>]] [-hbm [<.xpm>]] [-don [<.xvg>]]
13                    [-dan [<.xvg>]] [-life [<.xvg>]] [-nhbdist [<.xvg>]]
14                    [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
15                    [-xvg <enum>] [-a <real>] [-r <real>] [-[no]da]
16                    [-r2 <real>] [-abin <real>] [-rbin <real>] [-[no]nitacc]
17                    [-[no]contact] [-shell <real>] [-fitstart <real>]
18                    [-fitend <real>] [-temp <real>] [-dump <int>]
19                    [-max_hb <real>] [-[no]merge] [-acflen <int>]
20                    [-[no]normalize] [-P <enum>] [-fitfn <enum>]
21                    [-beginfit <real>] [-endfit <real>]
22

DESCRIPTION

24       gmx  hbond  computes  and  analyzes  hydrogen bonds. Hydrogen bonds are
25       determined based on cutoffs for the angle Hydrogen - Donor  -  Acceptor
26       (zero  is  extended)  and  the distance Donor - Acceptor (or Hydrogen -
27       Acceptor using -noda).  OH and NH groups are regarded as donors,  O  is
28       an  acceptor  always,  N  is  an  acceptor  by default, but this can be
29       switched using -nitacc. Dummy hydrogen atoms are  assumed  to  be  con‐
30       nected to the first preceding non-hydrogen atom.
31
32       You need to specify two groups for analysis, which must be either iden‐
33       tical or non-overlapping. All hydrogen bonds between the two groups are
34       analyzed.
35
36       If  you  set  -shell,  you  will be asked for an additional index group
37       which should contain exactly one atom.  In  this  case,  only  hydrogen
38       bonds  between  atoms  within  the shell distance from the one atom are
39       considered.
40
41       With option -ac, rate constants for hydrogen  bonding  can  be  derived
42       with  the  model  of  Luzar and Chandler (Nature 379:55, 1996; J. Chem.
43       Phys. 113:23, 2000).  If contact kinetics are  analyzed  by  using  the
44       -contact  option, then n(t) can be defined as either all pairs that are
45       not within contact distance r at time t (corresponding to  leaving  the
46       -r2  option  at  the default value 0) or all pairs that are within dis‐
47       tance r2 (corresponding to setting a second cut-off value  with  option
48       -r2).  See mentioned literature for more details and definitions.
49
50       Output:
51
52          · -num:  number of hydrogen bonds as a function of time.
53
54          · -ac:    average  over  all autocorrelations of the existence func‐
55            tions (either 0 or 1) of all hydrogen bonds.
56
57          · -dist: distance distribution of all hydrogen bonds.
58
59          · -ang:  angle distribution of all hydrogen bonds.
60
61          · -hx:   the number of n-n+i hydrogen bonds as a  function  of  time
62            where  n  and n+i stand for residue numbers and i ranges from 0 to
63            6.  This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds  asso‐
64            ciated with helices in proteins.
65
66          · -hbn:   all  selected  groups, donors, hydrogens and acceptors for
67            selected groups, all hydrogen bonded atoms from all groups and all
68            solvent atoms involved in insertion.
69
70          · -hbm:   existence  matrix  for all hydrogen bonds over all frames,
71            this also contains information on solvent insertion into  hydrogen
72            bonds. Ordering is identical to that in -hbn index file.
73
74          · -dan:  write  out  the number of donors and acceptors analyzed for
75            each timeframe. This is especially useful when using -shell.
76
77          · -nhbdist: compute the number of HBonds per hydrogen  in  order  to
78            compare results to Raman Spectroscopy.
79
80       Note:  options  -ac,  -life,  -hbn and -hbm require an amount of memory
81       proportional to the total numbers of donors times the total  number  of
82       acceptors in the selected group(s).
83

OPTIONS

85       Options to specify input files:
86
87       -f [<.xtc/.trr/…>] (traj.xtc)
88              Trajectory: xtc trr cpt gro g96 pdb tng
89
90       -s [<.tpr>] (topol.tpr)
91              Portable xdr run input file
92
93       -n [<.ndx>] (index.ndx) (Optional)
94              Index file
95
96       Options to specify output files:
97
98       -num [<.xvg>] (hbnum.xvg)
99              xvgr/xmgr file
100
101       -g [<.log>] (hbond.log) (Optional)
102              Log file
103
104       -ac [<.xvg>] (hbac.xvg) (Optional)
105              xvgr/xmgr file
106
107       -dist [<.xvg>] (hbdist.xvg) (Optional)
108              xvgr/xmgr file
109
110       -ang [<.xvg>] (hbang.xvg) (Optional)
111              xvgr/xmgr file
112
113       -hx [<.xvg>] (hbhelix.xvg) (Optional)
114              xvgr/xmgr file
115
116       -hbn [<.ndx>] (hbond.ndx) (Optional)
117              Index file
118
119       -hbm [<.xpm>] (hbmap.xpm) (Optional)
120              X PixMap compatible matrix file
121
122       -don [<.xvg>] (donor.xvg) (Optional)
123              xvgr/xmgr file
124
125       -dan [<.xvg>] (danum.xvg) (Optional)
126              xvgr/xmgr file
127
128       -life [<.xvg>] (hblife.xvg) (Optional)
129              xvgr/xmgr file
130
131       -nhbdist [<.xvg>] (nhbdist.xvg) (Optional)
132              xvgr/xmgr file
133
134       Other options:
135
136       -b <time> (0)
137              Time of first frame to read from trajectory (default unit ps)
138
139       -e <time> (0)
140              Time of last frame to read from trajectory (default unit ps)
141
142       -dt <time> (0)
143              Only use frame when t MOD dt = first time (default unit ps)
144
145       -tu <enum> (ps)
146              Unit for time values: fs, ps, ns, us, ms, s
147
148       -xvg <enum> (xmgrace)
149              xvg plot formatting: xmgrace, xmgr, none
150
151       -a <real> (30)
152              Cutoff angle (degrees, Hydrogen - Donor - Acceptor)
153
154       -r <real> (0.35)
155              Cutoff radius (nm, X - Acceptor, see next option)
156
157       -[no]da (yes)
158              Use  distance  Donor-Acceptor  (if  TRUE)  or  Hydrogen-Acceptor
159              (FALSE)
160
161       -r2 <real> (0)
162              Second cutoff radius. Mainly useful with -contact and -ac
163
164       -abin <real> (1)
165              Binwidth angle distribution (degrees)
166
167       -rbin <real> (0.005)
168              Binwidth distance distribution (nm)
169
170       -[no]nitacc (yes)
171              Regard nitrogen atoms as acceptors
172
173       -[no]contact (no)
174              Do not look for hydrogen bonds, but merely for  contacts  within
175              the cut-off distance
176
177       -shell <real> (-1)
178              when > 0, only calculate hydrogen bonds within # nm shell around
179              one particle
180
181       -fitstart <real> (1)
182              Time (ps) from which to start fitting the correlation  functions
183              in  order  to obtain the forward and backward rate constants for
184              HB breaking and formation. With -gemfit we suggest -fitstart 0
185
186       -fitend <real> (60)
187              Time (ps) to which to stop fitting the correlation functions  in
188              order  to  obtain the forward and backward rate constants for HB
189              breaking and formation (only with -gemfit)
190
191       -temp <real> (298.15)
192              Temperature (K) for computing the Gibbs energy corresponding  to
193              HB breaking and reforming
194
195       -dump <int> (0)
196              Dump  the  first  N hydrogen bond ACFs in a single .xvg file for
197              debugging
198
199       -max_hb <real> (0)
200              Theoretical maximum number of hydrogen bonds used for  normaliz‐
201              ing  HB autocorrelation function. Can be useful in case the pro‐
202              gram estimates it wrongly
203
204       -[no]merge (yes)
205              H-bonds between the same donor and acceptor, but with  different
206              hydrogen  are  treated  as a single H-bond. Mainly important for
207              the ACF.
208
209       -acflen <int> (-1)
210              Length of the ACF, default is half the number of frames
211
212       -[no]normalize (yes)
213              Normalize ACF
214
215       -P <enum> (0)
216              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
217              2, 3
218
219       -fitfn <enum> (none)
220              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
221
222       -beginfit <real> (0)
223              Time where to begin the exponential fit of the correlation func‐
224              tion
225
226       -endfit <real> (-1)
227              Time where to end the exponential fit of the  correlation  func‐
228              tion, -1 is until the end
229

KNOWN ISSUES

231       · The option -sel that used to work on selected hbonds is out of order,
232         and therefore not available for the time being.
233

SEE ALSO

235       gmx(1)
236
237       More    information    about    GROMACS    is    available    at     <‐
238       http://www.gromacs.org/>.
239
241       2019, GROMACS development team
242
243
244
245
2462019.2                           Apr 16, 2019                     GMX-HBOND(1)
Impressum