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 / integral from 0 to T of y^2(t) dt
44
45       This is useful for principal components obtained from covariance analy‐
46       sis,  since  the  principal  components  of  random  diffusion are pure
47       cosines.
48
49       Option -msd produces the mean square displacement(s).
50
51       Option -dist produces distribution plot(s).
52
53       Option -av produces the average over the sets.  Error bars can be added
54       with  the  option  -errbar.   The  errorbars can represent the standard
55       deviation, the error (assuming  the  points  are  independent)  or  the
56       interval  containing  90% of the points, by discarding 5% of the points
57       at the top and the bottom.
58
59       Option -ee produces error estimates using block averaging.   A  set  is
60       divided  in  a  number  of  blocks and averages are calculated for each
61       block. The error for the total average is calculated from the  variance
62       between  averages  of the m blocks B_i as follows: error^2 = sum (B_i -
63       <B>)^2 / (m*(m-1)).  These errors are plotted  as  a  function  of  the
64       block  size.  Also an analytical block average curve is plotted, assum‐
65       ing that the autocorrelation is a sum of two exponentials.  The analyt‐
66       ical curve for the block average is:
67
68          f(t) = sigma``*``sqrt(2/T (  alpha   (tau_1 ((exp(-t/tau_1) - 1) tau_1/t + 1)) +
69                                 (1-alpha) (tau_2 ((exp(-t/tau_2) - 1) tau_2/t + 1)))),
70
71       where T is the total time.  alpha, tau_1 and tau_2 are obtained by fit‐
72       ting f^2(t) to error^2.  When the actual block average is very close to
73       the  analytical curve, the error is sigma``*``sqrt(2/T (a tau_1 + (1-a)
74       tau_2)).  The complete derivation is given in B. Hess, J.  Chem.  Phys.
75       116:209-217, 2002.
76
77       Option  -filter  prints  the RMS high-frequency fluctuation of each set
78       and over all sets with respect to a filtered average.   The  filter  is
79       proportional to cos(pi t/len) where t goes from -len/2 to len/2. len is
80       supplied with the option -filter.   This  filter  reduces  oscillations
81       with period len/2 and len by a factor of 0.79 and 0.33 respectively.
82
83       Option -g fits the data to the function given with option -fitfn.
84
85       Option  -power fits the data to b t^a, which is accomplished by fitting
86       to a t + b on log-log scale. All points after the first zero or with  a
87       negative value are ignored.
88
89       Option  -luzar  performs a Luzar & Chandler kinetics analysis on output
90       from gmx hbond. The input file can be taken  directly  from  gmx  hbond
91       -ac, and then the same result should be produced.
92
93       Option  -fitfn  performs  curve fitting to a number of different curves
94       that make sense in the context of molecular dynamics,  mainly  exponen‐
95       tial  curves. More information is in the manual. To check the output of
96       the fitting procedure the option -fitted will print both  the  original
97       data and the fitted function to a new data file. The fitting parameters
98       are stored as comment in the output file.
99

OPTIONS

101       Options to specify input files:
102
103       -f [<.xvg>] (graph.xvg)
104              xvgr/xmgr file
105
106       Options to specify output files:
107
108       -ac [<.xvg>] (autocorr.xvg) (Optional)
109              xvgr/xmgr file
110
111       -msd [<.xvg>] (msd.xvg) (Optional)
112              xvgr/xmgr file
113
114       -cc [<.xvg>] (coscont.xvg) (Optional)
115              xvgr/xmgr file
116
117       -dist [<.xvg>] (distr.xvg) (Optional)
118              xvgr/xmgr file
119
120       -av [<.xvg>] (average.xvg) (Optional)
121              xvgr/xmgr file
122
123       -ee [<.xvg>] (errest.xvg) (Optional)
124              xvgr/xmgr file
125
126       -fitted [<.xvg>] (fitted.xvg) (Optional)
127              xvgr/xmgr file
128
129       -g [<.log>] (fitlog.log) (Optional)
130              Log file
131
132       Other options:
133
134       -[no]w (no)
135              View output .xvg, .xpm, .eps and .pdb files
136
137       -xvg <enum> (xmgrace)
138              xvg plot formatting: xmgrace, xmgr, none
139
140       -[no]time (yes)
141              Expect a time in the input
142
143       -b <real> (-1)
144              First time to read from set
145
146       -e <real> (-1)
147              Last time to read from set
148
149       -n <int> (1)
150              Read this number of sets separated by &
151
152       -[no]d (no)
153              Use the derivative
154
155       -bw <real> (0.1)
156              Binwidth for the distribution
157
158       -errbar <enum> (none)
159              Error bars for -av: none, stddev, error, 90
160
161       -[no]integrate (no)
162              Integrate data function(s) numerically using trapezium rule
163
164       -aver_start <real> (0)
165              Start averaging the integral from here
166
167       -[no]xydy (no)
168              Interpret second data set as error in the y values for integrat‐
169              ing
170
171       -[no]regression (no)
172              Perform  a  linear  regression analysis on the data. If -xydy is
173              set a second set will be interpreted as the error bar in  the  Y
174              value.  Otherwise, if multiple data sets are present a multilin‐
175              ear regression will be performed yielding the  constant  A  that
176              minimize  chi^2  = (y - A_0 x_0 - A_1 x_1 - … - A_N x_N)^2 where
177              now Y is the first data set in the input file and x_i  the  oth‐
178              ers. Do read the information at the option -time.
179
180       -[no]luzar (no)
181              Do  a  Luzar and Chandler analysis on a correlation function and
182              related as produced by gmx hbond. When  in  addition  the  -xydy
183              flag  is  given the second and fourth column will be interpreted
184              as errors in c(t) and n(t).
185
186       -temp <real> (298.15)
187              Temperature for the Luzar hydrogen bonding kinetics analysis (K)
188
189       -fitstart <real> (1)
190              Time (ps) from which to start fitting the correlation  functions
191              in  order  to obtain the forward and backward rate constants for
192              HB breaking and formation
193
194       -fitend <real> (60)
195              Time (ps) where to stop fitting  the  correlation  functions  in
196              order  to  obtain the forward and backward rate constants for HB
197              breaking and formation. Only with -gem
198
199       -filter <real> (0)
200              Print the high-frequency  fluctuation  after  filtering  with  a
201              cosine filter of this length
202
203       -[no]power (no)
204              Fit data to: b t^a
205
206       -[no]subav (yes)
207              Subtract the average before autocorrelating
208
209       -[no]oneacf (no)
210              Calculate one ACF over all sets
211
212       -acflen <int> (-1)
213              Length of the ACF, default is half the number of frames
214
215       -[no]normalize (yes)
216              Normalize ACF
217
218       -P <enum> (0)
219              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
220              2, 3
221
222       -fitfn <enum> (none)
223              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
224
225       -beginfit <real> (0)
226              Time where to begin the exponential fit of the correlation func‐
227              tion
228
229       -endfit <real> (-1)
230              Time  where  to end the exponential fit of the correlation func‐
231              tion, -1 is until the end
232

SEE ALSO

234       gmx(1)
235
236       More    information    about    GROMACS    is    available    at     <‐
237       http://www.gromacs.org/>.
238
240       2019, GROMACS development team
241
242
243
244
2452019.4                           Oct 02, 2019                   GMX-ANALYZE(1)
Impressum