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program-list.patch

documentation patch - Nicholas Breen, 08/03/2010 06:22 AM

View differences:

admin/mknroff.pl
25 25
	     "completion.zsh", "average", "completion.bash", "luck", 
26 26
	     "xplor2gmx.pl", "mptest", "ffscan", "demux.pl", "gentop", "mkyaw",
27 27
	     "tune_dip", "tune_pol", "hrefify", "options", "genvsites",
28
	     "pdtest", "bastat", "ehole" );
28
	     "pdtest", "bastat", "ehole", "GMXRC.bash", "GMXRC.csh",
29
             "GMXRC.zsh" );
29 30

  
30 31
%desc = ();
31 32
open(PPP,"$ptxt") || die("Can't open $ptxt");
32 33
$npp = 0;
33 34
while($line = <PPP>) {
34 35
  if ((index($line,"\|") > 0) && (index($line,"HEAD") < 0)) {
36
    $line =~ s/ -/ \\-/g;
35 37
    @tmp = split('\|',$line);
36 38
    if ($#tmp == 1) {
37 39
      if (!defined $desc{$tmp[0]}) {
admin/programs.txt
1 1
HEAD|Generating topologies and coordinates
2 2
pdb2gmx|converts pdb files to topology and coordinate files
3
x2top|generates a primitive topology from coordinates 
3
g_x2top|generates a primitive topology from coordinates 
4 4
editconf|edits the box and writes subgroups 
5 5
genbox|solvates a system
6 6
genion|generates mono atomic ions on energetically favorable positions
7 7
genconf|multiplies a conformation in 'random' orientations
8 8
genrestr|generates position restraints or distance restraints for index groups
9
protonate|protonates structures
9
g_protonate|protonates structures
10 10
END
11 11

  
12 12
HEAD|Running a simulation
......
17 17

  
18 18
HEAD|Viewing trajectories
19 19
ngmx|displays a trajectory
20
highway|X-windows gadget for highway simulations
20
g_highway|X Window System gadget for highway simulations
21
g_nmtraj|generate a virtual trajectory from an eigenvector
21 22
END
22 23

  
23 24
HEAD|Processing energies
......
31 32
trjconv|converts and manipulates trajectory files
32 33
trjcat|concatenates trajectory files
33 34
eneconv|converts energy files
34
xmp2ps|converts XPM matrices to encapsulated postscript (or XPM)
35
sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
35
xpm2ps|converts XPM matrices to encapsulated postscript (or XPM)
36
g_sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
36 37
END
37 38

  
38 39
HEAD|Tools
......
40 41
mk_angndx|generates index files for g_angle
41 42
gmxcheck|checks and compares files
42 43
gmxdump|makes binary files human readable
43
gen_table|generate tables for use by mdrun
44 44
g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory
45 45
g_analyze|analyzes data sets
46 46
trjorder|orders molecules according to their distance to a group
......
49 49
g_dyndom|interpolate and extrapolate structure rotations
50 50
g_morph|linear interpolation of conformations 
51 51
g_wham|weighted histogram analysis after umbrella sampling
52
ffscan|scan and modify force field data for a single point energy calculation
53 52
xpm2ps|convert XPM (XPixelMap) file to postscript
54 53
g_sham|read/write xmgr and xvgr data sets
55 54
g_spatial|calculates the spatial distribution function (more control than g_sdf)
56 55
g_sdf|calculates the spatial distribution function (faster than g_spatial)
57 56
g_select|selects groups of atoms based on flexible textual selections
57
g_tune_pme|time mdrun as a function of PME nodes to optimize settings
58 58
END
59 59

  
60 60
HEAD|Distances between structures
......
70 70
g_bond|calculates distances between atoms
71 71
g_mdmat|calculates residue contact maps
72 72
g_polystat|calculates static properties of polymers
73
g_rmsdist|calculates atom pair distances averaged with power 2, -3 or -6
73
g_rmsdist|calculates atom pair distances averaged with power -2, -3 or -6
74 74
END
75 75

  
76 76
HEAD|Mass distribution properties over time
......
79 79
g_msd|calculates mean square displacements
80 80
g_polystat|calculates static properties of polymers
81 81
g_rotacf|calculates the rotational correlation function for molecules
82
g_rdf|calculates radial distribution functions
82 83
g_rotmat|plots the rotation matrix for fitting to a reference structure
83 84
g_vanhove|calculates Van Hove displacement functions
84 85
END
......
104 105
g_bundle|analyzes bundles of axes, e.g. helices
105 106
g_disre|analyzes distance restraints
106 107
g_clustsize|calculate size distributions of atomic clusters
107
anadock|cluster structures from Autodock runs
108
g_anadock|cluster structures from Autodock runs
108 109
END
109 110

  
110 111
HEAD|Kinetic properties
111 112
g_traj|plots x, v, f, box, temperature and rotational energy
112 113
g_velacc|calculates velocity autocorrelation functions
113 114
g_tcaf|calculates viscosities of liquids
114
g_kinetics|derives information about kinetic processes from you trajectories
115
g_kinetics|derives information about kinetic processes from your trajectories
116
g_bar|calculates free energy difference estimates through Bennett's acceptance ratio
117
g_current|calculate current autocorrelation function of system
118
g_vanhove|compute Van Hove correlation function
119
g_principal|calculate principal axes of inertion for a group of atoms
115 120
END
116 121

  
117 122
HEAD|Electrostatic properties
......
120 125
g_dipoles|computes the total dipole plus fluctuations
121 126
g_dielectric|calculates frequency dependent dielectric constants
122 127
g_current|calculates dielectric constants for charged systems
128
g_spol|analyze dipoles around a solute
123 129
END
124 130

  
125 131
HEAD|Protein specific analysis
......
128 134
g_helix|calculates basic properties of alpha helices
129 135
g_helixorient|calculates local pitch/bending/rotation/orientation inside helices
130 136
g_rama|computes Ramachandran plots
131
xrama|shows animated Ramachandran plots
132
wheel|plots helical wheels
137
g_xrama|shows animated Ramachandran plots
138
g_wheel|plots helical wheels
133 139
END
134 140

  
135 141
HEAD|Interfaces
man/man7/gromacs.7
150 150
.IX Subsection "Generating topologies and coordinates"
151 151
.Vb 7
152 152
\&  pdb2gmx     converts pdb files to topology and coordinate files
153
\&  x2top       generates a primitive topology from coordinates
153
\&  g_x2top     generates a primitive topology from coordinates
154 154
\&  editconf    edits the box and writes subgroups
155 155
\&  genbox      solvates a system
156 156
\&  genion      generates mono atomic ions on energetically favorable positions
157 157
\&  genconf     multiplies a conformation in 'random' orientations
158
\&  protonate   protonates structures
158
\&  g_protonate protonates structures
159 159
.Ve
160 160
.Sh "Running a simulation"
161 161
.IX Subsection "Running a simulation"
162 162
.Vb 4
163 163
\&  grompp      makes a run input file
164 164
\&  tpbconv     makes a run input file for restarting a crashed run
165
\&  mdrun       performs a simulation
166
\&  mdrun_mpi   performs a sim across multiple CPUs or systems (in separate package)
165
\&  mdrun       performs a simulation, do a normal mode analysis or an energy minimization
166
\&  mdrun_mpi   performs a sim across multiple CPUs or systems
167 167
.Ve
168 168
.Sh "Viewing trajectories"
169 169
.IX Subsection "Viewing trajectories"
170 170
.Vb 3
171 171
\&  ngmx        displays a trajectory
172
\&  trjconv     converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
172
\&  g_highway   X Window System gadget for highway simulations
173 173
\&  g_nmtraj    generate a virtual trajectory from an eigenvector
174 174
.Ve                      
175 175
.Sh "Processing energies"
......
181 181
.Ve
182 182
.Sh "Converting files"
183 183
.IX Subsection "Converting files"
184
.Vb 5
184
.Vb 6
185 185
\&  editconf    converts and manipulates structure files
186 186
\&  trjconv     converts and manipulates trajectory files
187 187
\&  trjcat      concatenates trajectory files
188 188
\&  eneconv     converts energy files
189 189
\&  xpm2ps      converts XPM matrices to encapsulated postscript (or XPM)
190
\&  sigeps      convert c6/12 or c6/cn combinations to and from sigma/epsilon
190
\&  g_sigeps    convert c6/12 or c6/cn combinations to and from sigma/epsilon
191 191
.Ve
192 192
.Sh "Tools"
193 193
.IX Subsection "Tools"
......
199 199
\&  g_traj      plots x, v and f of selected atoms/groups (and more) from a trajectory
200 200
\&  g_analyze   analyzes data sets
201 201
\&  trjorder    orders molecules according to their distance to a group
202
\&  genrestr    generate topology include file with position restraints
203 202
\&  g_filter    frequency filters trajectories, useful for making smooth movies
204 203
\&  g_lie       free energy estimate from linear combinations
205 204
\&  g_dyndom    interpolate and extrapolate structure rotations
206 205
\&  g_morph     linear interpolation of conformations
207 206
\&  g_wham      weighted histogram analysis after umbrella sampling
208 207
\&  xpm2ps      convert XPM (XPixelMap) file to postscript
209
\&  g_densmap   compute 2D number-density maps and generate plots
210 208
\&  g_sham      read/write xmgr and xvgr data sets
211 209
\&  g_spatial   calculates the spatial distribution function (more control than g_sdf)
212 210
\&  g_sdf       calculates the spatial distribution function (faster than g_spatial)
211
\&  g_select    selects groups of atoms based on flexible textual selections
212
\&  g_tune_pme  time mdrun as a function of PME nodes to optimize settings
213 213
.Ve
214 214
.Sh "Distances between structures"
215 215
.IX Subsection "Distances between structures"
......
221 221
.Ve
222 222
.Sh "Distances in structures over time"
223 223
.IX Subsection "Distances in structures over time"
224
.Vb 5
224
.Vb 6
225 225
\&  g_mindist   calculates the minimum distance between two groups
226 226
\&  g_dist      calculates the distances between the centers of mass of two groups
227 227
\&  g_bond      calculates distances between atoms
228 228
\&  g_mdmat     calculates residue contact maps
229
\&  g_polystat  calculates static properties of polymers
229 230
\&  g_rmsdist   calculates atom pair distances averaged with power \-2, \-3 or \-6
230 231
.Ve
231 232
.Sh "Mass distribution properties over time"
232 233
.IX Subsection "Mass distribution properties over time"
233
.Vb 5
234
.Vb 8
234 235
\&  g_traj      plots x, v, f, box, temperature and rotational energy
235 236
\&  g_gyrate    calculates the radius of gyration
236 237
\&  g_msd       calculates mean square displacements
238
\&  g_polystat  calculates static properties of polymers
237 239
\&  g_rotacf    calculates the rotational correlation function for molecules
238 240
\&  g_rdf       calculates radial distribution functions
241
\&  g_rotmat    plots the rotation matrix for fitting to a reference structure
242
\&  g_vanhove   calculates Van Hove displacement functions
239 243
.Ve
240 244
.Sh "Analyzing bonded interactions"
241 245
.IX Subsection "Analyzing bonded interactions"
......
247 251
.Ve                      
248 252
.Sh "Structural properties"
249 253
.IX Subsection "Structural properties"
250
.Vb 11
254
.Vb 14
251 255
\&  g_hbond     computes and analyzes hydrogen bonds
252 256
\&  g_saltbr    computes salt bridges
253 257
\&  g_sas       computes solvent accessible surface area
254 258
\&  g_order     computes the order parameter per atom for carbon tails
259
\&  g_principal calculates axes of inertia for a group of atoms
260
\&  g_rdf       calculates radial distribution functions
261
\&  g_sdf       calculates solvent distribution functions
255 262
\&  g_sgangle   computes the angle and distance between two groups
256 263
\&  g_sorient   analyzes solvent orientation around solutes
264
\&  g_spol      analyzes solvent dipole orientation and polarization around solutes
257 265
\&  g_bundle    analyzes bundles of axes, e.g. helices
258 266
\&  g_disre     analyzes distance restraints
259 267
\&  g_clustsize calculate size distributions of atomic clusters
260
\&  anadock     cluster structures from Autodock runs
261
\&  g_polystat  plot average static properties of polymers
268
\&  g_anadock   cluster structures from Autodock runs
262 269
.Ve
263 270
.Sh "Kinetic properties"
264 271
.IX Subsection "Kinetic properties"
265
.Vb 7
272
.Vb 8
266 273
\&  g_traj      plots x, v, f, box, temperature and rotational energy
267 274
\&  g_velacc    calculates velocity autocorrelation functions
268 275
\&  g_tcaf      calculates viscosities of liquids
269 276
\&  g_kinetics  calculate kinetic rate constants (experimental)
277
\&  g_bar       calculates free energy difference estimates through Bennett's acceptance ratio
270 278
\&  g_current   calculate current autocorrelation function of system
271 279
\&  g_vanhove   compute Van Hove correlation function
272 280
\&  g_principal calculate principal axes of inertion for a group of atoms
273 281
.Ve                      
274 282
.Sh "Electrostatic properties"
275 283
.IX Subsection "Electrostatic properties"
276
.Vb 5
284
.Vb 6
277 285
\&  genion       generates mono atomic ions on energetically favorable positions
278 286
\&  g_potential  calculates the electrostatic potential across the box
279 287
\&  g_dipoles    computes the total dipole plus fluctuations
280 288
\&  g_dielectric calculates frequency dependent dielectric constants
289
\&  g_current    calculate current autocorrelation function of system
281 290
\&  g_spol       analyze dipoles around a solute
282 291
.Ve  
283 292
.Sh "Protein specific analysis"
......
288 297
\&  g_helix       calculates everything you want to know about helices
289 298
\&  g_helixorient calculate coordinates/directions of alpha-helix components
290 299
\&  g_rama        computes Ramachandran plots
291
\&  xrama         shows animated Ramachandran plots
300
\&  g_xrama       shows animated Ramachandran plots
292 301
\&  wheel         plots helical wheels
293 302
.Ve
294 303
.Sh "Interfaces"
295 304
.IX Subsection "Interfaces"
296
.Vb 5
305
.Vb 6
297 306
\&  g_potential calculates the electrostatic potential across the box
298 307
\&  g_density   calculates the density of the system
299 308
\&  g_order     computes the order parameter per atom for carbon tails
300 309
\&  g_h2order   computes the orientation of water molecules
301 310
\&  g_bundle    analyzes bundles of axes, e.g. transmembrane helices
311
\&  g_membed    embeds a protein into a lipid bilayer
302 312
.Ve                      
303 313
.Sh "Covariance analysis"
304 314
.IX Subsection "Covariance analysis"