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
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 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.
69 · -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 · -dan: write out the number of donors and acceptors analyzed for
75 each timeframe. This is especially useful when using -shell.
76 · -nhbdist: compute the number of HBonds per hydrogen in order to
78 compare results to Raman Spectroscopy.
79 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
85 Options to specify input files:
86 -f [<.xtc/.trr/…>] (traj.xtc)
88 Trajectory: xtc trr cpt gro g96 pdb tng
89 -s [<.tpr>] (topol.tpr)
91 Portable xdr run input file
92 -n [<.ndx>] (index.ndx) (Optional)
94 Index file
95 Options to specify output files:
97 -num [<.xvg>] (hbnum.xvg)
99 xvgr/xmgr file
100 -g [<.log>] (hbond.log) (Optional)
102 Log file
103 -ac [<.xvg>] (hbac.xvg) (Optional)
105 xvgr/xmgr file
106 -dist [<.xvg>] (hbdist.xvg) (Optional)
108 xvgr/xmgr file
109 -ang [<.xvg>] (hbang.xvg) (Optional)
111 xvgr/xmgr file
112 -hx [<.xvg>] (hbhelix.xvg) (Optional)
114 xvgr/xmgr file
115 -hbn [<.ndx>] (hbond.ndx) (Optional)
117 Index file
118 -hbm [<.xpm>] (hbmap.xpm) (Optional)
120 X PixMap compatible matrix file
121 -don [<.xvg>] (donor.xvg) (Optional)
123 xvgr/xmgr file
124 -dan [<.xvg>] (danum.xvg) (Optional)
126 xvgr/xmgr file
127 -life [<.xvg>] (hblife.xvg) (Optional)
129 xvgr/xmgr file
130 -nhbdist [<.xvg>] (nhbdist.xvg) (Optional)
132 xvgr/xmgr file
133 Other options:
135 -b <time> (0)
137 Time of first frame to read from trajectory (default unit ps)
138 -e <time> (0)
140 Time of last frame to read from trajectory (default unit ps)
141 -dt <time> (0)
143 Only use frame when t MOD dt = first time (default unit ps)
144 -tu <enum> (ps)
146 Unit for time values: fs, ps, ns, us, ms, s
147 -xvg <enum> (xmgrace)
149 xvg plot formatting: xmgrace, xmgr, none
150 -a <real> (30)
152 Cutoff angle (degrees, Hydrogen - Donor - Acceptor)
153 -r <real> (0.35)
155 Cutoff radius (nm, X - Acceptor, see next option)
156 -[no]da (yes)
158 Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor
159 (FALSE)
160 -r2 <real> (0)
162 Second cutoff radius. Mainly useful with -contact and -ac
163 -abin <real> (1)
165 Binwidth angle distribution (degrees)
166 -rbin <real> (0.005)
168 Binwidth distance distribution (nm)
169 -[no]nitacc (yes)
171 Regard nitrogen atoms as acceptors
172 -[no]contact (no)
174 Do not look for hydrogen bonds, but merely for contacts within
175 the cut-off distance
176 -shell <real> (-1)
178 when > 0, only calculate hydrogen bonds within # nm shell around
179 one particle
180 -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 -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 -temp <real> (298.15)
192 Temperature (K) for computing the Gibbs energy corresponding to
193 HB breaking and reforming
194 -dump <int> (0)
196 Dump the first N hydrogen bond ACFs in a single .xvg file for
197 debugging
198 -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 -[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 -acflen <int> (-1)
210 Length of the ACF, default is half the number of frames
211 -[no]normalize (yes)
213 Normalize ACF
214 -P <enum> (0)
216 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
217 2, 3
218 -fitfn <enum> (none)
220 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
221 -beginfit <real> (0)
223 Time where to begin the exponential fit of the correlation func‐
224 tion
225 -endfit <real> (-1)
227 Time where to end the exponential fit of the correlation func‐
228 tion, -1 is until the end
229
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
235 gmx(1)
236 More information about GROMACS is available at <‐
238 http://www.gromacs.org/>.
239
241 2019, GROMACS development team
2422019.2 Apr 16, 2019 GMX-HBOND(1)