1GMX-HBOND(1) GROMACS GMX-HBOND(1)
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6 gmx-hbond - Compute and analyze hydrogen bonds
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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
24 gmx hbond computes and analyzes hydrogen bonds. Hydrogen bonds are de‐
25 termined based on cutoffs for the angle Hydrogen - Donor - Acceptor
26 (zero is extended) and the distance Donor - Acceptor (or Hydrogen - Ac‐
27 ceptor using -noda). OH and NH groups are regarded as donors, O is an
28 acceptor always, N is an acceptor by default, but this can be switched
29 using -nitacc. Dummy hydrogen atoms are assumed to be connected to the
30 first preceding non-hydrogen atom.
31 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 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 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 Output:
51 • -num: number of hydrogen bonds as a function of time.
53 • -ac: average over all autocorrelations of the existence func‐
55 tions (either 0 or 1) of all hydrogen bonds.
56 • -dist: distance distribution of all hydrogen bonds.
58 • -ang: angle distribution of all hydrogen bonds.
60 • -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 • -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. Output is limited unless
69 -nomerge is set.
70 • -hbm: existence matrix for all hydrogen bonds over all frames,
72 this also contains information on solvent insertion into hydrogen
73 bonds. Ordering is identical to that in -hbn index file.
74 • -dan: write out the number of donors and acceptors analyzed for
76 each timeframe. This is especially useful when using -shell.
77 • -nhbdist: compute the number of HBonds per hydrogen in order to
79 compare results to Raman Spectroscopy.
80 Note: options -ac, -life, -hbn and -hbm require an amount of memory
82 proportional to the total numbers of donors times the total number of
83 acceptors in the selected group(s).
84
86 Options to specify input files:
87 -f [<.xtc/.trr/...>] (traj.xtc)
89 Trajectory: xtc trr cpt gro g96 pdb tng
90 -s [<.tpr>] (topol.tpr)
92 Portable xdr run input file
93 -n [<.ndx>] (index.ndx) (Optional)
95 Index file
96 Options to specify output files:
98 -num [<.xvg>] (hbnum.xvg)
100 xvgr/xmgr file
101 -g [<.log>] (hbond.log) (Optional)
103 Log file
104 -ac [<.xvg>] (hbac.xvg) (Optional)
106 xvgr/xmgr file
107 -dist [<.xvg>] (hbdist.xvg) (Optional)
109 xvgr/xmgr file
110 -ang [<.xvg>] (hbang.xvg) (Optional)
112 xvgr/xmgr file
113 -hx [<.xvg>] (hbhelix.xvg) (Optional)
115 xvgr/xmgr file
116 -hbn [<.ndx>] (hbond.ndx) (Optional)
118 Index file
119 -hbm [<.xpm>] (hbmap.xpm) (Optional)
121 X PixMap compatible matrix file
122 -don [<.xvg>] (donor.xvg) (Optional)
124 xvgr/xmgr file
125 -dan [<.xvg>] (danum.xvg) (Optional)
127 xvgr/xmgr file
128 -life [<.xvg>] (hblife.xvg) (Optional)
130 xvgr/xmgr file
131 -nhbdist [<.xvg>] (nhbdist.xvg) (Optional)
133 xvgr/xmgr file
134 Other options:
136 -b <time> (0)
138 Time of first frame to read from trajectory (default unit ps)
139 -e <time> (0)
141 Time of last frame to read from trajectory (default unit ps)
142 -dt <time> (0)
144 Only use frame when t MOD dt = first time (default unit ps)
145 -tu <enum> (ps)
147 Unit for time values: fs, ps, ns, us, ms, s
148 -xvg <enum> (xmgrace)
150 xvg plot formatting: xmgrace, xmgr, none
151 -a <real> (30)
153 Cutoff angle (degrees, Hydrogen - Donor - Acceptor)
154 -r <real> (0.35)
156 Cutoff radius (nm, X - Acceptor, see next option)
157 -[no]da (yes)
159 Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor
160 (FALSE)
161 -r2 <real> (0)
163 Second cutoff radius. Mainly useful with -contact and -ac
164 -abin <real> (1)
166 Binwidth angle distribution (degrees)
167 -rbin <real> (0.005)
169 Binwidth distance distribution (nm)
170 -[no]nitacc (yes)
172 Regard nitrogen atoms as acceptors
173 -[no]contact (no)
175 Do not look for hydrogen bonds, but merely for contacts within
176 the cut-off distance
177 -shell <real> (-1)
179 when > 0, only calculate hydrogen bonds within # nm shell around
180 one particle
181 -fitstart <real> (1)
183 Time (ps) from which to start fitting the correlation functions
184 in order to obtain the forward and backward rate constants for
185 HB breaking and formation. With -gemfit we suggest -fitstart 0
186 -fitend <real> (60)
188 Time (ps) to which to stop fitting the correlation functions in
189 order to obtain the forward and backward rate constants for HB
190 breaking and formation (only with -gemfit)
191 -temp <real> (298.15)
193 Temperature (K) for computing the Gibbs energy corresponding to
194 HB breaking and reforming
195 -dump <int> (0)
197 Dump the first N hydrogen bond ACFs in a single .xvg file for
198 debugging
199 -max_hb <real> (0)
201 Theoretical maximum number of hydrogen bonds used for normaliz‐
202 ing HB autocorrelation function. Can be useful in case the pro‐
203 gram estimates it wrongly
204 -[no]merge (yes)
206 H-bonds between the same donor and acceptor, but with different
207 hydrogen are treated as a single H-bond. Mainly important for
208 the ACF. Not compatible with options that depend on knowing a
209 specific hydrogen: -noad, -ang.
210 -acflen <int> (-1)
212 Length of the ACF, default is half the number of frames
213 -[no]normalize (yes)
215 Normalize ACF
216 -P <enum> (0)
218 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
219 2, 3
220 -fitfn <enum> (none)
222 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
223 -beginfit <real> (0)
225 Time where to begin the exponential fit of the correlation func‐
226 tion
227 -endfit <real> (-1)
229 Time where to end the exponential fit of the correlation func‐
230 tion, -1 is until the end
231
233 • The option -sel that used to work on selected hbonds is out of order,
234 and therefore not available for the time being.
235
237 gmx(1)
238 More information about GROMACS is available at <‐
240 http://www.gromacs.org/>.
241
243 2022, GROMACS development team
2442022.3 Sep 02, 2022 GMX-HBOND(1)