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1 .TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
2 .SH NAME
3 g_analyze - analyzes data sets
5 .B VERSION 4.5.4-dev-20110404-bc5695c
6 .SH SYNOPSIS
7 \f3g_analyze\fP
8 .BI "\-f" " graph.xvg "
9 .BI "\-ac" " autocorr.xvg "
10 .BI "\-msd" " msd.xvg "
11 .BI "\-cc" " coscont.xvg "
12 .BI "\-dist" " distr.xvg "
13 .BI "\-av" " average.xvg "
14 .BI "\-ee" " errest.xvg "
15 .BI "\-bal" " ballisitc.xvg "
16 .BI "\-g" " fitlog.log "
17 .BI "\-[no]h" ""
18 .BI "\-[no]version" ""
19 .BI "\-nice" " int "
20 .BI "\-[no]w" ""
21 .BI "\-xvg" " enum "
22 .BI "\-[no]time" ""
23 .BI "\-b" " real "
24 .BI "\-e" " real "
25 .BI "\-n" " int "
26 .BI "\-[no]d" ""
27 .BI "\-bw" " real "
28 .BI "\-errbar" " enum "
29 .BI "\-[no]integrate" ""
30 .BI "\-aver_start" " real "
31 .BI "\-[no]xydy" ""
32 .BI "\-[no]regression" ""
33 .BI "\-[no]luzar" ""
34 .BI "\-temp" " real "
35 .BI "\-fitstart" " real "
36 .BI "\-fitend" " real "
37 .BI "\-smooth" " real "
38 .BI "\-filter" " real "
39 .BI "\-[no]power" ""
40 .BI "\-[no]subav" ""
41 .BI "\-[no]oneacf" ""
42 .BI "\-acflen" " int "
43 .BI "\-[no]normalize" ""
44 .BI "\-P" " enum "
45 .BI "\-fitfn" " enum "
46 .BI "\-ncskip" " int "
47 .BI "\-beginfit" " real "
48 .BI "\-endfit" " real "
49 .SH DESCRIPTION
50 \&\fB g_analyze\fR reads an ASCII file and analyzes data sets.
51 \&A line in the input file may start with a time
52 \&(see option \fB \-time\fR) and any number of \fI y\fR\-values may follow.
53 \&Multiple sets can also be
54 \&read when they are separated by & (option \fB \-n\fR);
55 \&in this case only one \fI y\fR\-value is read from each line.
56 \&All lines starting with and @ are skipped.
57 \&All analyses can also be done for the derivative of a set
58 \&(option \fB \-d\fR).
61 \&All options, except for \fB \-av\fR and \fB \-power\fR, assume that the
62 \&points are equidistant in time.
65 \&\fB g_analyze\fR always shows the average and standard deviation of each
66 \&set, as well as the relative deviation of the third
67 \&and fourth cumulant from those of a Gaussian distribution with the same
68 \&standard deviation.
71 \&Option \fB \-ac\fR produces the autocorrelation function(s).
74 \&Option \fB \-cc\fR plots the resemblance of set i with a cosine of
75 \&i/2 periods. The formula is:
76 2 (int0\-T y(t) cos(i pi t) dt)2 / int0\-T y(t) y(t) dt
78 \&This is useful for principal components obtained from covariance
79 \&analysis, since the principal components of random diffusion are
80 \&pure cosines.
83 \&Option \fB \-msd\fR produces the mean square displacement(s).
86 \&Option \fB \-dist\fR produces distribution plot(s).
89 \&Option \fB \-av\fR produces the average over the sets.
90 \&Error bars can be added with the option \fB \-errbar\fR.
91 \&The errorbars can represent the standard deviation, the error
92 \&(assuming the points are independent) or the interval containing
93 \&90% of the points, by discarding 5% of the points at the top and
94 \&the bottom.
97 \&Option \fB \-ee\fR produces error estimates using block averaging.
98 \&A set is divided in a number of blocks and averages are calculated for
99 \&each block. The error for the total average is calculated from
100 \&the variance between averages of the m blocks B_i as follows:
101 \&error2 = Sum (B_i \- B)2 / (m*(m\-1)).
102 \&These errors are plotted as a function of the block size.
103 \&Also an analytical block average curve is plotted, assuming
104 \&that the autocorrelation is a sum of two exponentials.
105 \&The analytical curve for the block average is:
107 \&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) +
109 \& (1\-alpha) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))),
110 where T is the total time.
111 \&alpha, tau1 and tau2 are obtained by fitting f2(t) to error2.
112 \&When the actual block average is very close to the analytical curve,
113 \&the error is sigma\fB *\fRsqrt(2/T (a tau1 + (1\-a) tau2)).
114 \&The complete derivation is given in
115 \&B. Hess, J. Chem. Phys. 116:209\-217, 2002.
118 \&Option \fB \-bal\fR finds and subtracts the ultrafast "ballistic"
119 \&component from a hydrogen bond autocorrelation function by the fitting
120 \&of a sum of exponentials, as described in e.g.
121 \&O. Markovitch, J. Chem. Phys. 129:084505, 2008. The fastest term
122 \&is the one with the most negative coefficient in the exponential,
123 \&or with \fB \-d\fR, the one with most negative time derivative at time 0.
124 \&\fB \-nbalexp\fR sets the number of exponentials to fit.
127 \&Option \fB \-gem\fR fits bimolecular rate constants ka and kb
128 \&(and optionally kD) to the hydrogen bond autocorrelation function
129 \&according to the reversible geminate recombination model. Removal of
130 \&the ballistic component first is strongly adviced. The model is presented in
131 \&O. Markovitch, J. Chem. Phys. 129:084505, 2008.
134 \&Option \fB \-filter\fR prints the RMS high\-frequency fluctuation
135 \&of each set and over all sets with respect to a filtered average.
136 \&The filter is proportional to cos(pi t/len) where t goes from \-len/2
137 \&to len/2. len is supplied with the option \fB \-filter\fR.
138 \&This filter reduces oscillations with period len/2 and len by a factor
139 \&of 0.79 and 0.33 respectively.
142 \&Option \fB \-g\fR fits the data to the function given with option
143 \&\fB \-fitfn\fR.
146 \&Option \fB \-power\fR fits the data to b ta, which is accomplished
147 \&by fitting to a t + b on log\-log scale. All points after the first
148 \&zero or with a negative value are ignored.
150 Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis
151 \&on output from \fB g_hbond\fR. The input file can be taken directly
152 \&from \fB g_hbond \-ac\fR, and then the same result should be produced.
153 .SH FILES
154 .BI "\-f" " graph.xvg"
155 .B Input
156 xvgr/xmgr file
158 .BI "\-ac" " autocorr.xvg"
159 .B Output, Opt.
160 xvgr/xmgr file
162 .BI "\-msd" " msd.xvg"
163 .B Output, Opt.
164 xvgr/xmgr file
166 .BI "\-cc" " coscont.xvg"
167 .B Output, Opt.
168 xvgr/xmgr file
170 .BI "\-dist" " distr.xvg"
171 .B Output, Opt.
172 xvgr/xmgr file
174 .BI "\-av" " average.xvg"
175 .B Output, Opt.
176 xvgr/xmgr file
178 .BI "\-ee" " errest.xvg"
179 .B Output, Opt.
180 xvgr/xmgr file
182 .BI "\-bal" " ballisitc.xvg"
183 .B Output, Opt.
184 xvgr/xmgr file
186 .BI "\-g" " fitlog.log"
187 .B Output, Opt.
188 Log file
190 .SH OTHER OPTIONS
191 .BI "\-[no]h" "no "
192 Print help info and quit
194 .BI "\-[no]version" "no "
195 Print version info and quit
197 .BI "\-nice" " int" " 0"
198 Set the nicelevel
200 .BI "\-[no]w" "no "
201 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
203 .BI "\-xvg" " enum" " xmgrace"
204 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
206 .BI "\-[no]time" "yes "
207 Expect a time in the input
209 .BI "\-b" " real" " \-1 "
210 First time to read from set
212 .BI "\-e" " real" " \-1 "
213 Last time to read from set
215 .BI "\-n" " int" " 1"
216 Read sets separated by &
218 .BI "\-[no]d" "no "
219 Use the derivative
221 .BI "\-bw" " real" " 0.1 "
222 Binwidth for the distribution
224 .BI "\-errbar" " enum" " none"
225 Error bars for \fB \-av\fR: \fB none\fR, \fB stddev\fR, \fB error\fR or \fB 90\fR
227 .BI "\-[no]integrate" "no "
228 Integrate data function(s) numerically using trapezium rule
230 .BI "\-aver_start" " real" " 0 "
231 Start averaging the integral from here
233 .BI "\-[no]xydy" "no "
234 Interpret second data set as error in the y values for integrating
236 .BI "\-[no]regression" "no "
237 Perform a linear regression analysis on the data. If \fB \-xydy\fR is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi2 = (y \- A0 x0 \- A1 x1 \- ... \- AN xN)2 where now Y is the first data set in the input file and xi the others. Do read the information at the option \fB \-time\fR.
239 .BI "\-[no]luzar" "no "
240 Do a Luzar and Chandler analysis on a correlation function and related as produced by \fB g_hbond\fR. When in addition the \fB \-xydy\fR flag is given the second and fourth column will be interpreted as errors in c(t) and n(t).
242 .BI "\-temp" " real" " 298.15"
243 Temperature for the Luzar hydrogen bonding kinetics analysis
245 .BI "\-fitstart" " real" " 1 "
246 Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
248 .BI "\-fitend" " real" " 60 "
249 Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with \fB \-gem\fR
251 .BI "\-smooth" " real" " \-1 "
252 If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau)
254 .BI "\-filter" " real" " 0 "
255 Print the high\-frequency fluctuation after filtering with a cosine filter of length
257 .BI "\-[no]power" "no "
258 Fit data to: b ta
260 .BI "\-[no]subav" "yes "
261 Subtract the average before autocorrelating
263 .BI "\-[no]oneacf" "no "
264 Calculate one ACF over all sets
266 .BI "\-acflen" " int" " \-1"
267 Length of the ACF, default is half the number of frames
269 .BI "\-[no]normalize" "yes "
270 Normalize ACF
272 .BI "\-P" " enum" " 0"
273 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
275 .BI "\-fitfn" " enum" " none"
276 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
278 .BI "\-ncskip" " int" " 0"
279 Skip N points in the output file of correlation functions
281 .BI "\-beginfit" " real" " 0 "
282 Time where to begin the exponential fit of the correlation function
284 .BI "\-endfit" " real" " \-1 "
285 Time where to end the exponential fit of the correlation function, \-1 is until the end
287 .SH SEE ALSO
288 .BR gromacs(7)
290 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.