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gromacs-4.0/man/man1/anadock.1 2008-10-14 13:37:01.000000000 -0700
1
.TH anadock 1 "Mon 22 Sep 2008"
1
.TH anadock 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
2 2
.SH NAME
3
anadock
3
anadock \- cluster structures from Autodock runs
4 4
.B VERSION 4.0_rc1
5 5
.SH SYNOPSIS
6 6
\f3anadock\fP
7
.BI "-f" " eiwit.pdb "
8
.BI "-ox" " cluster.pdb "
9
.BI "-od" " edocked.xvg "
10
.BI "-of" " efree.xvg "
11
.BI "-g" " anadock.log "
12
.BI "-[no]h" ""
13
.BI "-nice" " int "
14
.BI "-[no]xvgr" ""
15
.BI "-[no]free" ""
16
.BI "-[no]rms" ""
17
.BI "-cutoff" " real "
7
.BI "\-f" " eiwit.pdb "
8
.BI "\-ox" " cluster.pdb "
9
.BI "\-od" " edocked.xvg "
10
.BI "\-of" " efree.xvg "
11
.BI "\-g" " anadock.log "
12
.BI "\-[no]h" ""
13
.BI "\-nice" " int "
14
.BI "\-[no]xvgr" ""
15
.BI "\-[no]free" ""
16
.BI "\-[no]rms" ""
17
.BI "\-cutoff" " real "
18 18
.SH DESCRIPTION
19 19
anadock analyses the results of an Autodock run and clusters the
20 20
structures together, based on distance or RMSD. The docked energy
......
28 28
and then sort the clusters on either lowest
29 29
energy or average energy.
30 30
.SH FILES
31
.BI "-f" " eiwit.pdb" 
31
.BI "\-f" " eiwit.pdb" 
32 32
.B Input
33 33
 Protein data bank file 
34 34

  
35
.BI "-ox" " cluster.pdb" 
35
.BI "\-ox" " cluster.pdb" 
36 36
.B Output
37 37
 Protein data bank file 
38 38

  
39
.BI "-od" " edocked.xvg" 
39
.BI "\-od" " edocked.xvg" 
40 40
.B Output
41 41
 xvgr/xmgr file 
42 42

  
43
.BI "-of" " efree.xvg" 
43
.BI "\-of" " efree.xvg" 
44 44
.B Output
45 45
 xvgr/xmgr file 
46 46

  
47
.BI "-g" " anadock.log" 
47
.BI "\-g" " anadock.log" 
48 48
.B Output
49 49
 Log file 
50 50

  
51 51
.SH OTHER OPTIONS
52
.BI "-[no]h"  "no    "
52
.BI "\-[no]h"  "no    "
53 53
 Print help info and quit
54 54

  
55
.BI "-nice"  " int" " 0" 
55
.BI "\-nice"  " int" " 0" 
56 56
 Set the nicelevel
57 57

  
58
.BI "-[no]xvgr"  "yes   "
58
.BI "\-[no]xvgr"  "yes   "
59 59
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
60 60

  
61
.BI "-[no]free"  "no    "
61
.BI "\-[no]free"  "no    "
62 62
 Use Free energy estimate from autodock for sorting the classes
63 63

  
64
.BI "-[no]rms"  "yes   "
64
.BI "\-[no]rms"  "yes   "
65 65
 Cluster on RMS or distance
66 66

  
67
.BI "-cutoff"  " real" " 0.2   " 
67
.BI "\-cutoff"  " real" " 0.2   " 
68 68
 Maximum RMSD/distance for belonging to the same cluster
69 69

  
70

  
71
.SH SEE ALSO
72
.BR gromacs(7)
73

  
74
More information about the \fBGROMACS\fR suite is available in \fB/usr/share/doc/gromacs\fR or at <\fIhttp://www.gromacs.org/\fR>.
gromacs-4.0/man/man1/do_dssp.1 2008-10-14 13:37:01.000000000 -0700
1
.TH do_dssp 1 "Mon 22 Sep 2008"
1
.TH do_dssp 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
2 2
.SH NAME
3
do_dssp
3
do_dssp \- assigns secondary structure and calculates solvent accessible surface area
4 4
.B VERSION 4.0_rc1
5 5
.SH SYNOPSIS
6 6
\f3do_dssp\fP
7
.BI "-f" " traj.xtc "
8
.BI "-s" " topol.tpr "
9
.BI "-n" " index.ndx "
10
.BI "-ssdump" " ssdump.dat "
11
.BI "-map" " ss.map "
12
.BI "-o" " ss.xpm "
13
.BI "-sc" " scount.xvg "
14
.BI "-a" " area.xpm "
15
.BI "-ta" " totarea.xvg "
16
.BI "-aa" " averarea.xvg "
17
.BI "-[no]h" ""
18
.BI "-nice" " int "
19
.BI "-b" " time "
20
.BI "-e" " time "
21
.BI "-dt" " time "
22
.BI "-tu" " enum "
23
.BI "-[no]w" ""
24
.BI "-[no]xvgr" ""
25
.BI "-sss" " string "
7
.BI "\-f" " traj.xtc "
8
.BI "\-s" " topol.tpr "
9
.BI "\-n" " index.ndx "
10
.BI "\-ssdump" " ssdump.dat "
11
.BI "\-map" " ss.map "
12
.BI "\-o" " ss.xpm "
13
.BI "\-sc" " scount.xvg "
14
.BI "\-a" " area.xpm "
15
.BI "\-ta" " totarea.xvg "
16
.BI "\-aa" " averarea.xvg "
17
.BI "\-[no]h" ""
18
.BI "\-nice" " int "
19
.BI "\-b" " time "
20
.BI "\-e" " time "
21
.BI "\-dt" " time "
22
.BI "\-tu" " enum "
23
.BI "\-[no]w" ""
24
.BI "\-[no]xvgr" ""
25
.BI "\-sss" " string "
26 26
.SH DESCRIPTION
27 27
do_dssp 
28 28
reads a trajectory file and computes the secondary structure for
......
32 32
/usr/local/bin/dssp. If this is not the case, then you should
33 33
set an environment variable 
34 34
.B DSSP
35
pointing to the dssp
36
executable, e.g.: 
37

  
38

  
35
pointing to the dssp executable, e.g.: 
39 36

  
40 37
.B setenv DSSP /opt/dssp/bin/dssp
41 38

  
......
52 49
.
53 50
The number of residues with each secondary structure type and the
54 51
total secondary structure (
55
.B -sss
52
.B \-sss
56 53
) count as a function of
57 54
time are also written to file (
58
.B -sc
55
.B \-sc
59 56
).
60 57

  
61 58

  
......
67 64
.B Note
68 65
that the program 
69 66
.B g_sas
70
can also compute SAS
71
and that is more efficient.
67
can also compute SAS and that is more efficient.
72 68

  
73 69

  
74 70
Finally, this program can dump the secondary structure in a special file
......
76 72
.B ssdump.dat
77 73
for usage in the program 
78 74
.B g_chi
79
. Together
75
\&. Together
80 76
these two programs can be used to analyze dihedral properties as a
81 77
function of secondary structure type.
82 78
.SH FILES
83
.BI "-f" " traj.xtc" 
79
.BI "\-f" " traj.xtc" 
84 80
.B Input
85 81
 Trajectory: xtc trr trj gro g96 pdb cpt 
86 82

  
87
.BI "-s" " topol.tpr" 
83
.BI "\-s" " topol.tpr" 
88 84
.B Input
89 85
 Structure+mass(db): tpr tpb tpa gro g96 pdb 
90 86

  
91
.BI "-n" " index.ndx" 
87
.BI "\-n" " index.ndx" 
92 88
.B Input, Opt.
93 89
 Index file 
94 90

  
95
.BI "-ssdump" " ssdump.dat" 
91
.BI "\-ssdump" " ssdump.dat" 
96 92
.B Output, Opt.
97 93
 Generic data file 
98 94

  
99
.BI "-map" " ss.map" 
95
.BI "\-map" " ss.map" 
100 96
.B Input, Lib.
101 97
 File that maps matrix data to colors 
102 98

  
103
.BI "-o" " ss.xpm" 
99
.BI "\-o" " ss.xpm" 
104 100
.B Output
105 101
 X PixMap compatible matrix file 
106 102

  
107
.BI "-sc" " scount.xvg" 
103
.BI "\-sc" " scount.xvg" 
108 104
.B Output
109 105
 xvgr/xmgr file 
110 106

  
111
.BI "-a" " area.xpm" 
107
.BI "\-a" " area.xpm" 
112 108
.B Output, Opt.
113 109
 X PixMap compatible matrix file 
114 110

  
115
.BI "-ta" " totarea.xvg" 
111
.BI "\-ta" " totarea.xvg" 
116 112
.B Output, Opt.
117 113
 xvgr/xmgr file 
118 114

  
119
.BI "-aa" " averarea.xvg" 
115
.BI "\-aa" " averarea.xvg" 
120 116
.B Output, Opt.
121 117
 xvgr/xmgr file 
122 118

  
123 119
.SH OTHER OPTIONS
124
.BI "-[no]h"  "no    "
120
.BI "\-[no]h"  "no    "
125 121
 Print help info and quit
126 122

  
127
.BI "-nice"  " int" " 19" 
123
.BI "\-nice"  " int" " 19" 
128 124
 Set the nicelevel
129 125

  
130
.BI "-b"  " time" " 0     " 
126
.BI "\-b"  " time" " 0     " 
131 127
 First frame (ps) to read from trajectory
132 128

  
133
.BI "-e"  " time" " 0     " 
129
.BI "\-e"  " time" " 0     " 
134 130
 Last frame (ps) to read from trajectory
135 131

  
136
.BI "-dt"  " time" " 0     " 
132
.BI "\-dt"  " time" " 0     " 
137 133
 Only use frame when t MOD dt = first time (ps)
138 134

  
139
.BI "-tu"  " enum" " ps" 
135
.BI "\-tu"  " enum" " ps" 
140 136
 Time unit: 
141 137
.B ps
142 138
, 
......
151 147
.B s
152 148

  
153 149

  
154
.BI "-[no]w"  "no    "
150
.BI "\-[no]w"  "no    "
155 151
 View output xvg, xpm, eps and pdb files
156 152

  
157
.BI "-[no]xvgr"  "yes   "
153
.BI "\-[no]xvgr"  "yes   "
158 154
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
159 155

  
160
.BI "-sss"  " string" " HEBT" 
156
.BI "\-sss"  " string" " HEBT" 
161 157
 Secondary structures for structure count
162 158

  
159

  
160
.SH SEE ALSO
161
.BR gromacs(7)
162

  
163
More information about the \fBGROMACS\fR suite is available in \fB/usr/share/doc/gromacs\fR or at <\fIhttp://www.gromacs.org/\fR>.
gromacs-4.0/man/man1/editconf.1 2008-10-14 13:37:01.000000000 -0700
1
.TH editconf 1 "Mon 22 Sep 2008"
1
.TH editconf 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
2 2
.SH NAME
3
editconf
3
editconf \- converts and manipulates structure files
4 4
.B VERSION 4.0_rc1
5 5
.SH SYNOPSIS
6 6
\f3editconf\fP
7
.BI "-f" " conf.gro "
8
.BI "-n" " index.ndx "
9
.BI "-o" " out.gro "
10
.BI "-mead" " mead.pqr "
11
.BI "-bf" " bfact.dat "
12
.BI "-[no]h" ""
13
.BI "-nice" " int "
14
.BI "-[no]w" ""
15
.BI "-[no]ndef" ""
16
.BI "-bt" " enum "
17
.BI "-box" " vector "
18
.BI "-angles" " vector "
19
.BI "-d" " real "
20
.BI "-[no]c" ""
21
.BI "-center" " vector "
22
.BI "-translate" " vector "
23
.BI "-rotate" " vector "
24
.BI "-[no]princ" ""
25
.BI "-scale" " vector "
26
.BI "-density" " real "
27
.BI "-[no]vol" ""
28
.BI "-[no]pbc" ""
29
.BI "-[no]grasp" ""
30
.BI "-rvdw" " real "
31
.BI "-sig56" " real "
32
.BI "-[no]vdwread" ""
33
.BI "-[no]atom" ""
34
.BI "-[no]legend" ""
35
.BI "-label" " string "
7
.BI "\-f" " conf.gro "
8
.BI "\-n" " index.ndx "
9
.BI "\-o" " out.gro "
10
.BI "\-mead" " mead.pqr "
11
.BI "\-bf" " bfact.dat "
12
.BI "\-[no]h" ""
13
.BI "\-nice" " int "
14
.BI "\-[no]w" ""
15
.BI "\-[no]ndef" ""
16
.BI "\-bt" " enum "
17
.BI "\-box" " vector "
18
.BI "\-angles" " vector "
19
.BI "\-d" " real "
20
.BI "\-[no]c" ""
21
.BI "\-center" " vector "
22
.BI "\-translate" " vector "
23
.BI "\-rotate" " vector "
24
.BI "\-[no]princ" ""
25
.BI "\-scale" " vector "
26
.BI "\-density" " real "
27
.BI "\-[no]vol" ""
28
.BI "\-[no]pbc" ""
29
.BI "\-[no]grasp" ""
30
.BI "\-rvdw" " real "
31
.BI "\-sig56" " real "
32
.BI "\-[no]vdwread" ""
33
.BI "\-[no]atom" ""
34
.BI "\-[no]legend" ""
35
.BI "\-label" " string "
36 36
.SH DESCRIPTION
37 37
editconf converts generic structure format to 
38 38
.B .gro
......
46 46

  
47 47

  
48 48
The box can be modified with options 
49
.B -box
49
.B \-box
50 50
, 
51
.B -d
51
.B \-d
52 52
and
53 53

  
54
.B -angles
55
. Both 
56
.B -box
54
.B \-angles
55
\&. Both 
56
.B \-box
57 57
and 
58
.B -d
58
.B \-d
59 59

  
60 60
will center the system in the box.
61 61

  
62 62

  
63 63

  
64 64
Option 
65
.B -bt
65
.B \-bt
66 66
determines the box type: 
67 67
.B triclinic
68 68
is a
......
83 83

  
84 84

  
85 85
Option 
86
.B -box
86
.B \-box
87 87
requires only
88 88
one value for a cubic box, dodecahedron and a truncated octahedron.
89 89

  
90 90

  
91 91

  
92 92
With 
93
.B -d
93
.B \-d
94 94
and a 
95 95
.B triclinic
96 96
box the size of the system in the x, y
97 97
and z directions is used. With 
98
.B -d
98
.B \-d
99 99
and 
100 100
.B cubic
101 101
,
......
110 110

  
111 111

  
112 112
Option 
113
.B -angles
113
.B \-angles
114 114
is only meaningful with option 
115
.B -box
115
.B \-box
116 116
and
117 117
a triclinic box and can not be used with option 
118
.B -d
118
.B \-d
119 119
.
120 120

  
121 121

  
122 122

  
123 123
When 
124
.B -n
124
.B \-n
125 125
or 
126
.B -ndef
126
.B \-ndef
127 127
is set, a group
128 128
can be selected for calculating the size and the geometric center,
129 129
otherwise the whole system is used.
......
131 131

  
132 132

  
133 133

  
134
.B -rotate
134
.B \-rotate
135 135
rotates the coordinates and velocities.
136 136

  
137 137

  
138 138

  
139 139

  
140
.B -princ
140
.B \-princ
141 141
aligns the principal axes of the system along the
142 142
coordinate axes, this may allow you to decrease the box volume,
143 143
but beware that molecules can rotate significantly in a nanosecond.
......
147 147
Scaling is applied before any of the other operations are
148 148
performed. Boxes can be scaled to give a certain density (option
149 149

  
150
.B -density
150
.B \-density
151 151
). A special feature of the scaling option, when the
152
factor -1 is given in one dimension, one obtains a mirror image,
153
mirrored in one of the plains, when one uses -1 in three dimensions
152
factor \-1 is given in one dimension, one obtains a mirror image,
153
mirrored in one of the plains, when one uses \-1 in three dimensions
154 154
a point-mirror image is obtained.
155 155

  
156 156

  
......
167 167
.B .pdb
168 168
files, B-factors can be
169 169
added with the 
170
.B -bf
170
.B \-bf
171 171
option. B-factors are read
172 172
from a file with with following format: first line states number of
173 173
entries in the file, next lines state an index
174 174
followed by a B-factor. The B-factors will be attached per residue
175 175
unless an index is larger than the number of residues or unless the
176 176

  
177
.B -atom
177
.B \-atom
178 178
option is set. Obviously, any type of numeric data can
179 179
be added instead of B-factors. 
180
.B -legend
180
.B \-legend
181 181
will produce
182 182
a row of CA atoms with B-factors ranging from the minimum to the
183 183
maximum value found, effectively making a legend for viewing.
184 184

  
185 185

  
186 186

  
187
With the option -mead a special pdb (pqr) file for the MEAD electrostatics
187
With the option \-mead a special pdb (pqr) file for the MEAD electrostatics
188 188
program (Poisson-Boltzmann solver) can be made. A further prerequisite
189 189
is that the input file is a run input file.
190 190
The B-factor field is then filled with the Van der Waals radius
......
192 192

  
193 193

  
194 194

  
195
The option -grasp is similar, but it puts the charges in the B-factor
195
The option \-grasp is similar, but it puts the charges in the B-factor
196 196
and the radius in the occupancy.
197 197

  
198 198

  
199 199

  
200 200
Finally with option 
201
.B -label
201
.B \-label
202 202
editconf can add a chain identifier
203 203
to a pdb file, which can be useful for analysis with e.g. rasmol.
204 204

  
......
207 207
a cubic box with the corners cut off (such as Gromos) use:
208 208

  
209 209

  
210
.B editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
210
.B editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out
211 211

  
212 212

  
213 213
where 
214 214
.B veclen
215 215
is the size of the cubic box times sqrt(3)/2.
216 216
.SH FILES
217
.BI "-f" " conf.gro" 
217
.BI "\-f" " conf.gro" 
218 218
.B Input
219 219
 Structure file: gro g96 pdb tpr tpb tpa 
220 220

  
221
.BI "-n" " index.ndx" 
221
.BI "\-n" " index.ndx" 
222 222
.B Input, Opt.
223 223
 Index file 
224 224

  
225
.BI "-o" " out.gro" 
225
.BI "\-o" " out.gro" 
226 226
.B Output, Opt.
227 227
 Structure file: gro g96 pdb 
228 228

  
229
.BI "-mead" " mead.pqr" 
229
.BI "\-mead" " mead.pqr" 
230 230
.B Output, Opt.
231 231
 Coordinate file for MEAD 
232 232

  
233
.BI "-bf" " bfact.dat" 
233
.BI "\-bf" " bfact.dat" 
234 234
.B Input, Opt.
235 235
 Generic data file 
236 236

  
237 237
.SH OTHER OPTIONS
238
.BI "-[no]h"  "no    "
238
.BI "\-[no]h"  "no    "
239 239
 Print help info and quit
240 240

  
241
.BI "-nice"  " int" " 0" 
241
.BI "\-nice"  " int" " 0" 
242 242
 Set the nicelevel
243 243

  
244
.BI "-[no]w"  "no    "
244
.BI "\-[no]w"  "no    "
245 245
 View output xvg, xpm, eps and pdb files
246 246

  
247
.BI "-[no]ndef"  "no    "
247
.BI "\-[no]ndef"  "no    "
248 248
 Choose output from default index groups
249 249

  
250
.BI "-bt"  " enum" " triclinic" 
251
 Box type for -box and -d: 
250
.BI "\-bt"  " enum" " triclinic" 
251
 Box type for \-box and \-d: 
252 252
.B triclinic
253 253
, 
254 254
.B cubic
......
258 258
.B octahedron
259 259

  
260 260

  
261
.BI "-box"  " vector" " 0 0 0" 
261
.BI "\-box"  " vector" " 0 0 0" 
262 262
 Box vector lengths (a,b,c)
263 263

  
264
.BI "-angles"  " vector" " 90 90 90" 
264
.BI "\-angles"  " vector" " 90 90 90" 
265 265
 Angles between the box vectors (bc,ac,ab)
266 266

  
267
.BI "-d"  " real" " 0     " 
267
.BI "\-d"  " real" " 0     " 
268 268
 Distance between the solute and the box
269 269

  
270
.BI "-[no]c"  "no    "
271
 Center molecule in box (implied by -box and -d)
270
.BI "\-[no]c"  "no    "
271
 Center molecule in box (implied by \-box and \-d)
272 272

  
273
.BI "-center"  " vector" " 0 0 0" 
273
.BI "\-center"  " vector" " 0 0 0" 
274 274
 Coordinates of geometrical center
275 275

  
276
.BI "-translate"  " vector" " 0 0 0" 
276
.BI "\-translate"  " vector" " 0 0 0" 
277 277
 Translation
278 278

  
279
.BI "-rotate"  " vector" " 0 0 0" 
279
.BI "\-rotate"  " vector" " 0 0 0" 
280 280
 Rotation around the X, Y and Z axes in degrees
281 281

  
282
.BI "-[no]princ"  "no    "
282
.BI "\-[no]princ"  "no    "
283 283
 Orient molecule(s) along their principal axes
284 284

  
285
.BI "-scale"  " vector" " 1 1 1" 
285
.BI "\-scale"  " vector" " 1 1 1" 
286 286
 Scaling factor
287 287

  
288
.BI "-density"  " real" " 1000  " 
288
.BI "\-density"  " real" " 1000  " 
289 289
 Density (g/l) of the output box achieved by scaling
290 290

  
291
.BI "-[no]vol"  "yes   "
291
.BI "\-[no]vol"  "yes   "
292 292
 Compute and print volume of the box
293 293

  
294
.BI "-[no]pbc"  "no    "
294
.BI "\-[no]pbc"  "no    "
295 295
 Remove the periodicity (make molecule whole again)
296 296

  
297
.BI "-[no]grasp"  "no    "
297
.BI "\-[no]grasp"  "no    "
298 298
 Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
299 299

  
300
.BI "-rvdw"  " real" " 0.12  " 
300
.BI "\-rvdw"  " real" " 0.12  " 
301 301
 Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
302 302

  
303
.BI "-sig56"  " real" " 0     " 
303
.BI "\-sig56"  " real" " 0     " 
304 304
 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 
305 305

  
306
.BI "-[no]vdwread"  "no    "
306
.BI "\-[no]vdwread"  "no    "
307 307
 Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
308 308

  
309
.BI "-[no]atom"  "no    "
309
.BI "\-[no]atom"  "no    "
310 310
 Force B-factor attachment per atom
311 311

  
312
.BI "-[no]legend"  "no    "
312
.BI "\-[no]legend"  "no    "
313 313
 Make B-factor legend
314 314

  
315
.BI "-label"  " string" " A" 
315
.BI "\-label"  " string" " A" 
316 316
 Add chain label for all residues
317 317

  
318 318
.SH KNOWN PROBLEMS
319 319
\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
320 320

  
321

  
322
.SH SEE ALSO
323
.BR gromacs(7)
324

  
325
More information about the \fBGROMACS\fR suite is available in \fB/usr/share/doc/gromacs\fR or at <\fIhttp://www.gromacs.org/\fR>.
gromacs-4.0/man/man1/eneconv.1 2008-10-14 13:37:01.000000000 -0700
1
.TH eneconv 1 "Mon 22 Sep 2008"
1
.TH eneconv 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
2 2
.SH NAME
3
eneconv
3
eneconv \- converts energy files
4 4
.B VERSION 4.0_rc1
5 5
.SH SYNOPSIS
6 6
\f3eneconv\fP
7
.BI "-f" " ener.edr "
8
.BI "-o" " fixed.edr "
9
.BI "-[no]h" ""
10
.BI "-nice" " int "
11
.BI "-b" " real "
12
.BI "-e" " real "
13
.BI "-dt" " real "
14
.BI "-offset" " real "
15
.BI "-[no]settime" ""
16
.BI "-[no]sort" ""
17
.BI "-scalefac" " real "
18
.BI "-[no]error" ""
7
.BI "\-f" " ener.edr "
8
.BI "\-o" " fixed.edr "
9
.BI "\-[no]h" ""
10
.BI "\-nice" " int "
11
.BI "\-b" " real "
12
.BI "\-e" " real "
13
.BI "\-dt" " real "
14
.BI "\-offset" " real "
15
.BI "\-[no]settime" ""
16
.BI "\-[no]sort" ""
17
.BI "\-scalefac" " real "
18
.BI "\-[no]error" ""
19 19
.SH DESCRIPTION
20 20
With 
21 21
.I multiple files
22 22
specified for the 
23
.B -f
23
.B \-f
24 24
option:
25 25

  
26 26
Concatenates several energy files in sorted order.
27 27
In case of double time frames the one
28 28
in the later file is used. By specifying 
29
.B -settime
29
.B \-settime
30 30
you will be
31 31
asked for the start time of each file. The input files are taken
32 32
from the command line,
33 33
such that the command 
34
.B eneconv -o fixed.edr *.edr
34
.B eneconv \-o fixed.edr *.edr
35 35
should do
36 36
the trick. 
37 37

  
......
39 39
With 
40 40
.I one file
41 41
specified for 
42
.B -f
42
.B \-f
43 43
:
44 44

  
45 45
Reads one energy file and writes another, applying the 
46
.B -dt
46
.B \-dt
47 47
,
48 48

  
49
.B -offset
49
.B \-offset
50 50
, 
51
.B -t0
51
.B \-t0
52 52
and 
53
.B -settime
53
.B \-settime
54 54
options and
55 55
converting to a different format if necessary (indicated by file
56 56
extentions).
57 57

  
58 58

  
59 59

  
60
.B -settime
60
.B \-settime
61 61
is applied first, then 
62
.B -dt
62
.B \-dt
63 63
/
64
.B -offset
64
.B \-offset
65 65

  
66 66
followed by 
67
.B -b
67
.B \-b
68 68
and 
69
.B -e
69
.B \-e
70 70
to select which frames to write.
71 71
.SH FILES
72
.BI "-f" " ener.edr" 
72
.BI "\-f" " ener.edr" 
73 73
.B Input, Mult.
74 74
 Energy file: edr ene 
75 75

  
76
.BI "-o" " fixed.edr" 
76
.BI "\-o" " fixed.edr" 
77 77
.B Output
78 78
 Energy file: edr ene 
79 79

  
80 80
.SH OTHER OPTIONS
81
.BI "-[no]h"  "no    "
81
.BI "\-[no]h"  "no    "
82 82
 Print help info and quit
83 83

  
84
.BI "-nice"  " int" " 19" 
84
.BI "\-nice"  " int" " 19" 
85 85
 Set the nicelevel
86 86

  
87
.BI "-b"  " real" " -1    " 
87
.BI "\-b"  " real" " \-1    " 
88 88
 First time to use
89 89

  
90
.BI "-e"  " real" " -1    " 
90
.BI "\-e"  " real" " \-1    " 
91 91
 Last time to use
92 92

  
93
.BI "-dt"  " real" " 0     " 
93
.BI "\-dt"  " real" " 0     " 
94 94
 Only write out frame when t MOD dt = offset
95 95

  
96
.BI "-offset"  " real" " 0     " 
97
 Time offset for -dt option
96
.BI "\-offset"  " real" " 0     " 
97
 Time offset for \-dt option
98 98

  
99
.BI "-[no]settime"  "no    "
99
.BI "\-[no]settime"  "no    "
100 100
 Change starting time interactively
101 101

  
102
.BI "-[no]sort"  "yes   "
102
.BI "\-[no]sort"  "yes   "
103 103
 Sort energy files (not frames)
104 104

  
105
.BI "-scalefac"  " real" " 1     " 
105
.BI "\-scalefac"  " real" " 1     " 
106 106
 Multiply energy component by this factor
107 107

  
108
.BI "-[no]error"  "yes   "
108
.BI "\-[no]error"  "yes   "
109 109
 Stop on errors in the file
110 110

  
111 111
.SH KNOWN PROBLEMS
112 112
\- When combining trajectories the sigma and E2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
113 113

  
114

  
115
.SH SEE ALSO
116
.BR gromacs(7)
117

  
118
More information about the \fBGROMACS\fR suite is available in \fB/usr/share/doc/gromacs\fR or at <\fIhttp://www.gromacs.org/\fR>.
gromacs-4.0/man/man1/g_anaeig.1 2008-10-14 13:37:01.000000000 -0700
1
.TH g_anaeig 1 "Mon 22 Sep 2008"
1
.TH g_anaeig 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
2 2
.SH NAME
3
g_anaeig
3
g_anaeig \- analyzes the eigenvectors and normal modes
4 4
.B VERSION 4.0_rc1
5 5
.SH SYNOPSIS
6 6
\f3g_anaeig\fP
7
.BI "-v" " eigenvec.trr "
8
.BI "-v2" " eigenvec2.trr "
9
.BI "-f" " traj.xtc "
10
.BI "-s" " topol.tpr "
11
.BI "-n" " index.ndx "
12
.BI "-eig" " eigenval.xvg "
13
.BI "-eig2" " eigenval2.xvg "
14
.BI "-comp" " eigcomp.xvg "
15
.BI "-rmsf" " eigrmsf.xvg "
16
.BI "-proj" " proj.xvg "
17
.BI "-2d" " 2dproj.xvg "
18
.BI "-3d" " 3dproj.pdb "
19
.BI "-filt" " filtered.xtc "
20
.BI "-extr" " extreme.pdb "
21
.BI "-over" " overlap.xvg "
22
.BI "-inpr" " inprod.xpm "
23
.BI "-[no]h" ""
24
.BI "-nice" " int "
25
.BI "-b" " time "
26
.BI "-e" " time "
27
.BI "-dt" " time "
28
.BI "-tu" " enum "
29
.BI "-[no]w" ""
30
.BI "-[no]xvgr" ""
31
.BI "-first" " int "
32
.BI "-last" " int "
33
.BI "-skip" " int "
34
.BI "-max" " real "
35
.BI "-nframes" " int "
36
.BI "-[no]split" ""
37
.BI "-[no]entropy" ""
38
.BI "-temp" " real "
39
.BI "-nevskip" " int "
7
.BI "\-v" " eigenvec.trr "
8
.BI "\-v2" " eigenvec2.trr "
9
.BI "\-f" " traj.xtc "
10
.BI "\-s" " topol.tpr "
11
.BI "\-n" " index.ndx "
12
.BI "\-eig" " eigenval.xvg "
13
.BI "\-eig2" " eigenval2.xvg "
14
.BI "\-comp" " eigcomp.xvg "
15
.BI "\-rmsf" " eigrmsf.xvg "
16
.BI "\-proj" " proj.xvg "
17
.BI "\-2d" " 2dproj.xvg "
18
.BI "\-3d" " 3dproj.pdb "
19
.BI "\-filt" " filtered.xtc "
20
.BI "\-extr" " extreme.pdb "
21
.BI "\-over" " overlap.xvg "
22
.BI "\-inpr" " inprod.xpm "
23
.BI "\-[no]h" ""
24
.BI "\-nice" " int "
25
.BI "\-b" " time "
26
.BI "\-e" " time "
27
.BI "\-dt" " time "
28
.BI "\-tu" " enum "
29
.BI "\-[no]w" ""
30
.BI "\-[no]xvgr" ""
31
.BI "\-first" " int "
32
.BI "\-last" " int "
33
.BI "\-skip" " int "
34
.BI "\-max" " real "
35
.BI "\-nframes" " int "
36
.BI "\-[no]split" ""
37
.BI "\-[no]entropy" ""
38
.BI "\-temp" " real "
39
.BI "\-nevskip" " int "
40 40
.SH DESCRIPTION
41 41

  
42 42
.B g_anaeig
......
54 54
to the structure in the structure file. When no run input file is
55 55
supplied, periodicity will not be taken into account. Most analyses
56 56
are performed on eigenvectors 
57
.B -first
57
.B \-first
58 58
to 
59
.B -last
59
.B \-last
60 60
, but when
61 61

  
62
.B -first
63
is set to -1 you will be prompted for a selection.
62
.B \-first
63
is set to \-1 you will be prompted for a selection.
64 64

  
65 65

  
66 66

  
67
.B -comp
67
.B \-comp
68 68
: plot the vector components per atom of eigenvectors
69 69

  
70
.B -first
70
.B \-first
71 71
to 
72
.B -last
72
.B \-last
73 73
.
74 74

  
75 75

  
76 76

  
77
.B -rmsf
77
.B \-rmsf
78 78
: plot the RMS fluctuation per atom of eigenvectors
79 79

  
80
.B -first
80
.B \-first
81 81
to 
82
.B -last
82
.B \-last
83 83
(requires 
84
.B -eig
84
.B \-eig
85 85
).
86 86

  
87 87

  
88 88

  
89
.B -proj
89
.B \-proj
90 90
: calculate projections of a trajectory on eigenvectors
91 91

  
92
.B -first
92
.B \-first
93 93
to 
94
.B -last
94
.B \-last
95 95
.
96 96
The projections of a trajectory on the eigenvectors of its
97 97
covariance matrix are called principal components (pc's).
......
105 105

  
106 106

  
107 107

  
108
.B -2d
108
.B \-2d
109 109
: calculate a 2d projection of a trajectory on eigenvectors
110 110

  
111
.B -first
111
.B \-first
112 112
and 
113
.B -last
113
.B \-last
114 114
.
115 115

  
116 116

  
117 117

  
118
.B -3d
119
: calculate a 3d projection of a trajectory on the first
120
three selected eigenvectors.
118
.B \-3d
119
: calculate a 3d projection of a trajectory on the first three selected eigenvectors.
121 120

  
122 121

  
123 122

  
124
.B -filt
125
: filter the trajectory to show only the motion along
126
eigenvectors 
127
.B -first
123
.B \-filt
124
: filter the trajectory to show only the motion along eigenvectors 
125
.B \-first
128 126
to 
129
.B -last
127
.B \-last
130 128
.
131 129

  
132 130

  
133 131

  
134
.B -extr
132
.B \-extr
135 133
: calculate the two extreme projections along a trajectory
136 134
on the average structure and interpolate 
137
.B -nframes
135
.B \-nframes
138 136
frames
139 137
between them, or set your own extremes with 
140
.B -max
141
. The
138
.B \-max
139
\&. The
142 140
eigenvector 
143
.B -first
141
.B \-first
144 142
will be written unless 
145
.B -first
143
.B \-first
146 144
and
147 145

  
148
.B -last
146
.B \-last
149 147
have been set explicitly, in which case all eigenvectors
150 148
will be written to separate files. Chain identifiers will be added
151 149
when writing a 
152 150
.B .pdb
153 151
file with two or three structures (you
154 152
can use 
155
.B rasmol -nmrpdb
153
.B rasmol \-nmrpdb
156 154
to view such a pdb file).
157 155

  
158 156

  
......
162 160

  
163 161

  
164 162

  
165
.B -over
163
.B \-over
166 164
: calculate the subspace overlap of the eigenvectors in
167 165
file 
168
.B -v2
166
.B \-v2
169 167
with eigenvectors 
170
.B -first
168
.B \-first
171 169
to 
172
.B -last
170
.B \-last
173 171

  
174 172
in file 
175
.B -v
173
.B \-v
176 174
.
177 175

  
178 176

  
179 177

  
180
.B -inpr
178
.B \-inpr
181 179
: calculate a matrix of inner-products between
182 180
eigenvectors in files 
183
.B -v
181
.B \-v
184 182
and 
185
.B -v2
186
. All eigenvectors
183
.B \-v2
184
\&. All eigenvectors
187 185
of both files will be used unless 
188
.B -first
186
.B \-first
189 187
and 
190
.B -last
188
.B \-last
191 189

  
192 190
have been set explicitly.
193 191

  
194 192

  
195 193
When 
196
.B -v
194
.B \-v
197 195
, 
198
.B -eig
196
.B \-eig
199 197
, 
200
.B -v2
198
.B \-v2
201 199
and 
202
.B -eig2
200
.B \-eig2
203 201
are given,
204 202
a single number for the overlap between the covariance matrices is
205 203
generated. The formulas are:
206 204

  
207
        difference = sqrt(tr((sqrt(M1) - sqrt(M2))2))
205
        difference = sqrt(tr((sqrt(M1) \- sqrt(M2))2))
208 206

  
209
normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
207
normalized overlap = 1 \- difference/sqrt(tr(M1) + tr(M2))
210 208

  
211
     shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))2))
209
     shape overlap = 1 \- sqrt(tr((sqrt(M1/tr(M1)) \- sqrt(M2/tr(M2)))2))
212 210

  
213 211
where M1 and M2 are the two covariance matrices and tr is the trace
214 212
of a matrix. The numbers are proportional to the overlap of the square
......
218 216

  
219 217

  
220 218
When the 
221
.B -entropy
219
.B \-entropy
222 220
flag is given an entropy estimate will be
223 221
computed based on the Quasiharmonic approach and based on
224 222
Schlitter's formula.
225 223
.SH FILES
226
.BI "-v" " eigenvec.trr" 
224
.BI "\-v" " eigenvec.trr" 
227 225
.B Input
228 226
 Full precision trajectory: trr trj cpt 
229 227

  
230
.BI "-v2" " eigenvec2.trr" 
228
.BI "\-v2" " eigenvec2.trr" 
231 229
.B Input, Opt.
232 230
 Full precision trajectory: trr trj cpt 
233 231

  
234
.BI "-f" " traj.xtc" 
232
.BI "\-f" " traj.xtc" 
235 233
.B Input, Opt.
236 234
 Trajectory: xtc trr trj gro g96 pdb cpt 
237 235

  
238
.BI "-s" " topol.tpr" 
236
.BI "\-s" " topol.tpr" 
239 237
.B Input, Opt.
240 238
 Structure+mass(db): tpr tpb tpa gro g96 pdb 
241 239

  
242
.BI "-n" " index.ndx" 
240
.BI "\-n" " index.ndx" 
243 241
.B Input, Opt.
244 242
 Index file 
245 243

  
246
.BI "-eig" " eigenval.xvg" 
244
.BI "\-eig" " eigenval.xvg" 
247 245
.B Input, Opt.
248 246
 xvgr/xmgr file 
249 247

  
250
.BI "-eig2" " eigenval2.xvg" 
248
.BI "\-eig2" " eigenval2.xvg" 
251 249
.B Input, Opt.
252 250
 xvgr/xmgr file 
253 251

  
254
.BI "-comp" " eigcomp.xvg" 
252
.BI "\-comp" " eigcomp.xvg" 
255 253
.B Output, Opt.
256 254
 xvgr/xmgr file 
257 255

  
258
.BI "-rmsf" " eigrmsf.xvg" 
256
.BI "\-rmsf" " eigrmsf.xvg" 
259 257
.B Output, Opt.
260 258
 xvgr/xmgr file 
261 259

  
262
.BI "-proj" " proj.xvg" 
260
.BI "\-proj" " proj.xvg" 
263 261
.B Output, Opt.
264 262
 xvgr/xmgr file 
265 263

  
266
.BI "-2d" " 2dproj.xvg" 
264
.BI "\-2d" " 2dproj.xvg" 
267 265
.B Output, Opt.
268 266
 xvgr/xmgr file 
269 267

  
270
.BI "-3d" " 3dproj.pdb" 
268
.BI "\-3d" " 3dproj.pdb" 
271 269
.B Output, Opt.
272 270
 Structure file: gro g96 pdb 
273 271

  
274
.BI "-filt" " filtered.xtc" 
272
.BI "\-filt" " filtered.xtc" 
275 273
.B Output, Opt.
276 274
 Trajectory: xtc trr trj gro g96 pdb cpt 
277 275

  
278
.BI "-extr" " extreme.pdb" 
276
.BI "\-extr" " extreme.pdb" 
279 277
.B Output, Opt.
280 278
 Trajectory: xtc trr trj gro g96 pdb cpt 
281 279

  
282
.BI "-over" " overlap.xvg" 
280
.BI "\-over" " overlap.xvg" 
283 281
.B Output, Opt.
284 282
 xvgr/xmgr file 
285 283

  
286
.BI "-inpr" " inprod.xpm" 
284
.BI "\-inpr" " inprod.xpm" 
287 285
.B Output, Opt.
288 286
 X PixMap compatible matrix file 
289 287

  
290 288
.SH OTHER OPTIONS
291
.BI "-[no]h"  "no    "
289
.BI "\-[no]h"  "no    "
292 290
 Print help info and quit
293 291

  
294
.BI "-nice"  " int" " 19" 
292
.BI "\-nice"  " int" " 19" 
295 293
 Set the nicelevel
296 294

  
297
.BI "-b"  " time" " 0     " 
295
.BI "\-b"  " time" " 0     " 
298 296
 First frame (ps) to read from trajectory
299 297

  
300
.BI "-e"  " time" " 0     " 
298
.BI "\-e"  " time" " 0     " 
301 299
 Last frame (ps) to read from trajectory
302 300

  
303
.BI "-dt"  " time" " 0     " 
301
.BI "\-dt"  " time" " 0     " 
304 302
 Only use frame when t MOD dt = first time (ps)
305 303

  
306
.BI "-tu"  " enum" " ps" 
304
.BI "\-tu"  " enum" " ps" 
307 305
 Time unit: 
308 306
.B ps
309 307
, 
......
318 316
.B s
319 317

  
320 318

  
321
.BI "-[no]w"  "no    "
319
.BI "\-[no]w"  "no    "
322 320
 View output xvg, xpm, eps and pdb files
323 321

  
324
.BI "-[no]xvgr"  "yes   "
322
.BI "\-[no]xvgr"  "yes   "
325 323
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
326 324

  
327
.BI "-first"  " int" " 1" 
328
 First eigenvector for analysis (-1 is select)
325
.BI "\-first"  " int" " 1" 
326
 First eigenvector for analysis (\-1 is select)
329 327

  
330
.BI "-last"  " int" " 8" 
331
 Last eigenvector for analysis (-1 is till the last)
328
.BI "\-last"  " int" " 8" 
329
 Last eigenvector for analysis (\-1 is till the last)
332 330

  
333
.BI "-skip"  " int" " 1" 
331
.BI "\-skip"  " int" " 1" 
334 332
 Only analyse every nr-th frame
335 333

  
336
.BI "-max"  " real" " 0     " 
334
.BI "\-max"  " real" " 0     " 
337 335
 Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes
338 336

  
339
.BI "-nframes"  " int" " 2" 
337
.BI "\-nframes"  " int" " 2" 
340 338
 Number of frames for the extremes output
341 339

  
342
.BI "-[no]split"  "no    "
340
.BI "\-[no]split"  "no    "
343 341
 Split eigenvector projections where time is zero
344 342

  
345
.BI "-[no]entropy"  "no    "
343
.BI "\-[no]entropy"  "no    "
346 344
 Compute entropy according to the Quasiharmonic formula or Schlitter's method.
347 345

  
348
.BI "-temp"  " real" " 298.15" 
346
.BI "\-temp"  " real" " 298.15" 
349 347
 Temperature for entropy calculations
350 348

  
351
.BI "-nevskip"  " int" " 6" 
349
.BI "\-nevskip"  " int" " 6" 
352 350
 Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy.
353 351

  
352

  
353
.SH SEE ALSO
354
.BR gromacs(7)
355

  
356
More information about the \fBGROMACS\fR suite is available in \fB/usr/share/doc/gromacs\fR or at <\fIhttp://www.gromacs.org/\fR>.
gromacs-4.0/man/man1/g_analyze.1 2008-10-14 13:37:48.000000000 -0700
1
.TH g_analyze 1 "Mon 22 Sep 2008"
1
.TH g_analyze 1 "Mon 22 Sep 2008" "" "GROMACS suite, Version 4.0"
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.SH NAME
3
g_analyze
3
g_analyze \- analyzes data sets
4 4
.B VERSION 4.0_rc1
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.SH SYNOPSIS
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\f3g_analyze\fP
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.BI "-f" " graph.xvg "
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.BI "-ac" " autocorr.xvg "
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.BI "-msd" " msd.xvg "
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.BI "-cc" " coscont.xvg "
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.BI "-dist" " distr.xvg "
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.BI "-av" " average.xvg "
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.BI "-ee" " errest.xvg "
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.BI "-g" " fitlog.log "
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.BI "-[no]h" ""
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.BI "-nice" " int "
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.BI "-[no]w" ""
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.BI "-[no]xvgr" ""
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.BI "-[no]time" ""
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.BI "-b" " real "
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.BI "-e" " real "
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.BI "-n" " int "
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.BI "-[no]d" ""
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.BI "-bw" " real "
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.BI "-errbar" " enum "
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.BI "-[no]integrate" ""
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.BI "-aver_start" " real "
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.BI "-[no]xydy" ""
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.BI "-[no]regression" ""
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.BI "-[no]luzar" ""
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.BI "-temp" " real "
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.BI "-fitstart" " real "
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.BI "-smooth" " real "
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.BI "-filter" " real "
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.BI "-[no]power" ""
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.BI "-[no]subav" ""
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.BI "-[no]oneacf" ""
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.BI "-acflen" " int "
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.BI "-[no]normalize" ""
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.BI "-P" " enum "
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.BI "-fitfn" " enum "
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.BI "-ncskip" " int "
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.BI "-beginfit" " real "
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.BI "-endfit" " real "
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.BI "\-f" " graph.xvg "
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.BI "\-ac" " autocorr.xvg "
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.BI "\-msd" " msd.xvg "
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.BI "\-cc" " coscont.xvg "
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.BI "\-dist" " distr.xvg "
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.BI "\-av" " average.xvg "
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.BI "\-ee" " errest.xvg "
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.BI "\-g" " fitlog.log "
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.BI "\-[no]h" ""
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.BI "\-nice" " int "
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.BI "\-[no]w" ""
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.BI "\-[no]xvgr" ""
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.BI "\-[no]time" ""
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.BI "\-b" " real "
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.BI "\-e" " real "
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.BI "\-n" " int "
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.BI "\-[no]d" ""
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.BI "\-bw" " real "
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.BI "\-errbar" " enum "
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.BI "\-[no]integrate" ""
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.BI "\-aver_start" " real "
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.BI "\-[no]xydy" ""
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.BI "\-[no]regression" ""
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.BI "\-[no]luzar" ""
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.BI "\-temp" " real "
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.BI "\-fitstart" " real "
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.BI "\-smooth" " real "
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.BI "\-filter" " real "
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.BI "\-[no]power" ""
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.BI "\-[no]subav" ""
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.BI "\-[no]oneacf" ""
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.BI "\-acflen" " int "
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.BI "\-[no]normalize" ""
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.BI "\-P" " enum "
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.BI "\-fitfn" " enum "
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.BI "\-ncskip" " int "
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.BI "\-beginfit" " real "
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.BI "\-endfit" " real "
45 45
.SH DESCRIPTION
46 46
g_analyze reads an ascii file and analyzes data sets.
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A line in the input file may start with a time
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(see option 
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.B -time
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.B \-time
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) and any number of y values may follow.
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Multiple sets can also be
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read when they are seperated by & (option 
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.B -n
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.B \-n
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),
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in this case only one y value is read from each line.
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All lines starting with  and @ are skipped.
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All analyses can also be done for the derivative of a set
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(option 
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.B -d
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.B \-d
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).
61 61

  
62 62

  
63 63
All options, except for 
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.B -av
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.B \-av
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and 
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.B -power
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.B \-power
67 67
assume that the
68 68
points are equidistant in time.
69 69

  
......
75 75

  
76 76

  
77 77
Option 
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.B -ac
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.B \-ac
79 79
produces the autocorrelation function(s).
80 80

  
81 81

  
82 82
Option 
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.B -cc
83
.B \-cc
84 84
plots the resemblance of set i with a cosine of
85 85
i/2 periods. The formula is:
86 86
2 (int0-T y(t) cos(i pi t) dt)2 / int0-T y(t) y(t) dt
......
91 91

  
92 92

  
93 93
Option 
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.B -msd
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.B \-msd
95 95
produces the mean square displacement(s).
96 96

  
97 97

  
98 98
Option 
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.B -dist
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.B \-dist
100 100
produces distribution plot(s).
101 101

  
102 102

  
103 103
Option 
104
.B -av
104
.B \-av
105 105
produces the average over the sets.
106 106
Error bars can be added with the option 
107
.B -errbar
107
.B \-errbar
108 108
.
109 109
The errorbars can represent the standard deviation, the error
110 110
(assuming the points are independent) or the interval containing
......
113 113

  
114 114

  
115 115
Option 
116
.B -ee
116
.B \-ee
117 117
produces error estimates using block averaging.
118 118
A set is divided in a number of blocks and averages are calculated for
119 119
each block. The error for the total average is calculated from
120 120
the variance between averages of the m blocks B_i as follows:
121
error2 = Sum (B_i - B)2 / (m*(m-1)).
121
error2 = Sum (B_i \- B)2 / (m*(m\-1)).
122 122
These errors are plotted as a function of the block size.
123 123
Also an analytical block average curve is plotted, assuming
124 124
that the autocorrelation is a sum of two exponentials.
125 125
The analytical curve for the block average is:
126 126

  
127
f(t) = sigma sqrt(2/T (  a   (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +
127
f(t) = sigma sqrt(2/T (  a   (tau1 ((exp(\-t/tau1) \-1) tau1/t + 1)) +
128 128

  
129
                       (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),
129
                       (1\-a) (tau2 ((exp(\-t/tau2) \-1) tau2/t + 1)))),
130 130
where T is the total time.
131 131
a, tau1 and tau2 are obtained by fitting f2(t) to error2.
132 132
When the actual block average is very close to the analytical curve,
133
the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
133
the error is sigma*sqrt(2/T (a tau1 + (1\-a) tau2)).
134 134
The complete derivation is given in
135 135
B. Hess, J. Chem. Phys. 116:209-217, 2002.
136 136

  
137 137

  
138 138
Option 
139
.B -filter
139
.B \-filter
140 140
prints the RMS high-frequency fluctuation
141 141
of each set and over all sets with respect to a filtered average.
142
The filter is proportional to cos(pi t/len) where t goes from -len/2
142
The filter is proportional to cos(pi t/len) where t goes from \-len/2
143 143
to len/2. len is supplied with the option 
144
.B -filter
144
.B \-filter
145 145
.
146 146
This filter reduces oscillations with period len/2 and len by a factor
147 147
of 0.79 and 0.33 respectively.
148 148

  
149 149

  
150 150
Option 
151
.B -g
151
.B \-g
152 152
fits the data to the function given with option
153 153

  
154
.B -fitfn
154
.B \-fitfn
155 155
.
156 156

  
157 157

  
158 158
Option 
159
.B -power
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