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

NAME

6       gmx-analyze - Analyze data sets
7

SYNOPSIS

9          gmx analyze [-f [<.xvg>]] [-ac [<.xvg>]] [-msd [<.xvg>]] [-cc [<.xvg>]]
10                      [-dist [<.xvg>]] [-av [<.xvg>]] [-ee [<.xvg>]]
11                      [-fitted [<.xvg>]] [-g [<.log>]] [-[no]w] [-xvg <enum>]
12                      [-[no]time] [-b <real>] [-e <real>] [-n <int>] [-[no]d]
13                      [-bw <real>] [-errbar <enum>] [-[no]integrate]
14                      [-aver_start <real>] [-[no]xydy] [-[no]regression]
15                      [-[no]luzar] [-temp <real>] [-fitstart <real>]
16                      [-fitend <real>] [-filter <real>] [-[no]power]
17                      [-[no]subav] [-[no]oneacf] [-acflen <int>]
18                      [-[no]normalize] [-P <enum>] [-fitfn <enum>]
19                      [-beginfit <real>] [-endfit <real>]
20

DESCRIPTION

22       gmx  analyze reads an ASCII file and analyzes data sets.  A line in the
23       input file may start with a time (see option -time) and any  number  of
24       y-values may follow.  Multiple sets can also be read when they are sep‐
25       arated by & (option -n); in this case only one  y-value  is  read  from
26       each  line.  All lines starting with # and @ are skipped.  All analyses
27       can also be done for the derivative of a set (option -d).
28
29       All options, except for -av and -power,  assume  that  the  points  are
30       equidistant in time.
31
32       gmx  analyze  always  shows  the average and standard deviation of each
33       set, as well as the relative deviation of the third and fourth cumulant
34       from those of a Gaussian distribution with the same standard deviation.
35
36       Option  -ac produces the autocorrelation function(s).  Be sure that the
37       time interval between data points is much shorter than the  time  scale
38       of the autocorrelation.
39
40       Option -cc plots the resemblance of set i with a cosine of i/2 periods.
41       The formula is:
42
43          2 (integral from 0 to T of y(t) cos(i pi t) dt)^2
44          / integral from 0 to T of y^2(t) dt
45
46       This is useful for principal components obtained from covariance analy‐
47       sis,  since  the  principal  components  of  random  diffusion are pure
48       cosines.
49
50       Option -msd produces the mean square displacement(s).
51
52       Option -dist produces distribution plot(s).
53
54       Option -av produces the average over the sets.  Error bars can be added
55       with  the option -errbar.  The errorbars can represent the standard de‐
56       viation, the error (assuming the points are independent) or the  inter‐
57       val containing 90% of the points, by discarding 5% of the points at the
58       top and the bottom.
59
60       Option -ee produces error estimates using block averaging.   A  set  is
61       divided  in  a  number  of  blocks and averages are calculated for each
62       block. The error for the total average is calculated from the  variance
63       between  averages  of the m blocks B_i as follows: error^2 = sum (B_i -
64       <B>)^2 / (m*(m-1)).  These errors are plotted  as  a  function  of  the
65       block  size.  Also an analytical block average curve is plotted, assum‐
66       ing that the autocorrelation is a sum of two exponentials.  The analyt‐
67       ical curve for the block average is:
68
69          f(t) = sigma``*``sqrt(2/T (  alpha
70          (tau_1 ((exp(-t/tau_1) - 1)
71          tau_1/t + 1)) +
72          (1-alpha) (tau_2
73          ((exp(-t/tau_2) - 1) tau_2/t +
74          1)))),
75
76       where T is the total time.  alpha, tau_1 and tau_2 are obtained by fit‐
77       ting f^2(t) to error^2.  When the actual block average is very close to
78       the  analytical curve, the error is sigma``*``sqrt(2/T (a tau_1 + (1-a)
79       tau_2)).  The complete derivation is given in B. Hess, J.  Chem.  Phys.
80       116:209-217, 2002.
81
82       Option  -filter  prints  the RMS high-frequency fluctuation of each set
83       and over all sets with respect to a filtered average.   The  filter  is
84       proportional to cos(pi t/len) where t goes from -len/2 to len/2. len is
85       supplied with the option -filter.   This  filter  reduces  oscillations
86       with period len/2 and len by a factor of 0.79 and 0.33 respectively.
87
88       Option -g fits the data to the function given with option -fitfn.
89
90       Option  -power fits the data to b t^a, which is accomplished by fitting
91       to a t + b on log-log scale. All points after the first zero or with  a
92       negative value are ignored.
93
94       Option  -luzar  performs a Luzar & Chandler kinetics analysis on output
95       from gmx hbond. The input file can be taken  directly  from  gmx  hbond
96       -ac, and then the same result should be produced.
97
98       Option  -fitfn  performs  curve fitting to a number of different curves
99       that make sense in the context of molecular dynamics,  mainly  exponen‐
100       tial  curves. More information is in the manual. To check the output of
101       the fitting procedure the option -fitted will print both  the  original
102       data and the fitted function to a new data file. The fitting parameters
103       are stored as comment in the output file.
104

OPTIONS

106       Options to specify input files:
107
108       -f [<.xvg>] (graph.xvg)
109              xvgr/xmgr file
110
111       Options to specify output files:
112
113       -ac [<.xvg>] (autocorr.xvg) (Optional)
114              xvgr/xmgr file
115
116       -msd [<.xvg>] (msd.xvg) (Optional)
117              xvgr/xmgr file
118
119       -cc [<.xvg>] (coscont.xvg) (Optional)
120              xvgr/xmgr file
121
122       -dist [<.xvg>] (distr.xvg) (Optional)
123              xvgr/xmgr file
124
125       -av [<.xvg>] (average.xvg) (Optional)
126              xvgr/xmgr file
127
128       -ee [<.xvg>] (errest.xvg) (Optional)
129              xvgr/xmgr file
130
131       -fitted [<.xvg>] (fitted.xvg) (Optional)
132              xvgr/xmgr file
133
134       -g [<.log>] (fitlog.log) (Optional)
135              Log file
136
137       Other options:
138
139       -[no]w (no)
140              View output .xvg, .xpm, .eps and .pdb files
141
142       -xvg <enum> (xmgrace)
143              xvg plot formatting: xmgrace, xmgr, none
144
145       -[no]time (yes)
146              Expect a time in the input
147
148       -b <real> (-1)
149              First time to read from set
150
151       -e <real> (-1)
152              Last time to read from set
153
154       -n <int> (1)
155              Read this number of sets separated by &
156
157       -[no]d (no)
158              Use the derivative
159
160       -bw <real> (0.1)
161              Binwidth for the distribution
162
163       -errbar <enum> (none)
164              Error bars for -av: none, stddev, error, 90
165
166       -[no]integrate (no)
167              Integrate data function(s) numerically using trapezium rule
168
169       -aver_start <real> (0)
170              Start averaging the integral from here
171
172       -[no]xydy (no)
173              Interpret second data set as error in the y values for integrat‐
174              ing
175
176       -[no]regression (no)
177              Perform  a  linear  regression analysis on the data. If -xydy is
178              set a second set will be interpreted as the error bar in  the  Y
179              value.  Otherwise, if multiple data sets are present a multilin‐
180              ear regression will be performed yielding the  constant  A  that
181              minimize chi^2 = (y - A_0 x_0 - A_1 x_1 - ... - A_N x_N)^2 where
182              now Y is the first data set in the input file and x_i  the  oth‐
183              ers. Do read the information at the option -time.
184
185       -[no]luzar (no)
186              Do  a  Luzar and Chandler analysis on a correlation function and
187              related as produced by gmx hbond. When  in  addition  the  -xydy
188              flag  is  given the second and fourth column will be interpreted
189              as errors in c(t) and n(t).
190
191       -temp <real> (298.15)
192              Temperature for the Luzar hydrogen bonding kinetics analysis (K)
193
194       -fitstart <real> (1)
195              Time (ps) from which to start fitting the correlation  functions
196              in  order  to obtain the forward and backward rate constants for
197              HB breaking and formation
198
199       -fitend <real> (60)
200              Time (ps) where to stop fitting the correlation functions in or‐
201              der  to  obtain  the  forward and backward rate constants for HB
202              breaking and formation. Only with -gem
203
204       -filter <real> (0)
205              Print the high-frequency fluctuation after filtering with a  co‐
206              sine filter of this length
207
208       -[no]power (no)
209              Fit data to: b t^a
210
211       -[no]subav (yes)
212              Subtract the average before autocorrelating
213
214       -[no]oneacf (no)
215              Calculate one ACF over all sets
216
217       -acflen <int> (-1)
218              Length of the ACF, default is half the number of frames
219
220       -[no]normalize (yes)
221              Normalize ACF
222
223       -P <enum> (0)
224              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
225              2, 3
226
227       -fitfn <enum> (none)
228              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
229
230       -beginfit <real> (0)
231              Time where to begin the exponential fit of the correlation func‐
232              tion
233
234       -endfit <real> (-1)
235              Time  where  to end the exponential fit of the correlation func‐
236              tion, -1 is until the end
237

SEE ALSO

239       gmx(1)
240
241       More    information    about    GROMACS    is    available    at     <‐
242       http://www.gromacs.org/>.
243
245       2022, GROMACS development team
246
247
248
249
2502022.2                           Jun 16, 2022                   GMX-ANALYZE(1)
Impressum